NCBI Gallus gallus Annotation Release 106
The RefSeq genome records for Gallus gallus were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.
The annotation products are available in the sequence databases and on the FTP site.
This report provides:
- Annotation Release information: The name of the release, important dates, the software version
- Assemblies: A brief description of the annotated assembly(ies)
- Gene and feature statistics: The counts and characteristics of the annotated features
- BUSCO results: Annotation completeness assessed with BUSCO
- Alignment of the annotated proteins to a set of high-quality proteins: The number of annotated proteins with hits to a set of high-quality proteins
- Masking of genomic sequence: How much of the genome was masked
- Transcript and protein alignments: The number and type of evidence retrieved from public databases and used for gene prediction
- Similarity of current and previous assembly: The similarity of the current and previous assembly
- Similarity of alternate and reference assemblies: The similarity of the alternate assemblies to the reference
- Comparison of the current and previous annotations: What proportion of the genes changed in this annotation
For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.
Annotation Release information
This annotation should be referred to as NCBI Gallus gallus Annotation Release 106Annotation release ID: 106
Date of Entrez queries for transcripts and proteins: Dec 23 2021
Date of submission of annotation to the public databases: Mar 3 2022
Software version: 9.0
Assemblies
The following assemblies were included in this annotation run:Assembly name | Assembly accession | Submitter | Assembly date | Reference/Alternate | Assembly content |
---|---|---|---|---|---|
bGalGal1.mat.broiler.GRCg7b | GCF_016699485.2 | Vertebrate Genomes Project | 01-19-2021 | Reference | 42 assembled chromosomes; unplaced scaffolds |
bGalGal1.pat.whiteleghornlayer.GRCg7w | GCF_016700215.2 | Vertebrate Genomes Project | 10-01-2021 | Alternate | 41 assembled chromosomes; unplaced scaffolds |
Gene and feature statistics
Counts and length of annotated features are provided below for each assembly.Feature counts
Feature | bGalGal1.mat.broiler.GRCg7b | bGalGal1.pat.whiteleghornlayer.GRCg7w |
---|---|---|
Genes and pseudogenes | 25,635 | 25,564 |
protein-coding | 18,023 | 17,981 |
non-coding | 7,330 | 7,310 |
Transcribed pseudogenes | 26 | 27 |
Non-transcribed pseudogenes | 172 | 123 |
genes with variants | 12,408 | 12,278 |
Immunoglobulin/T-cell receptor gene segments | 70 | 108 |
other | 14 | 15 |
mRNAs | 68,670 | 68,341 |
fully-supported | 64,886 | 64,467 |
with > 5% ab initio | 518 | 501 |
partial | 253 | 302 |
with filled gap(s) | 13 | 19 |
known RefSeq (NM_) | 8,379 | 8,351 |
model RefSeq (XM_) | 60,291 | 59,990 |
non-coding RNAs | 16,124 | 16,135 |
fully-supported | 14,982 | 15,003 |
with > 5% ab initio | 0 | 0 |
partial | 2 | 1 |
with filled gap(s) | 0 | 0 |
known RefSeq (NR_) | 939 | 948 |
model RefSeq (XR_) | 14,471 | 14,514 |
pseudo transcripts | 26 | 27 |
fully-supported | 21 | 24 |
with > 5% ab initio | 0 | 0 |
partial | 0 | 0 |
with filled gap(s) | 0 | 0 |
known RefSeq (NR_) | 6 | 6 |
model RefSeq (XR_) | 20 | 21 |
CDSs | 68,753 | 68,449 |
fully-supported | 64,886 | 64,467 |
with > 5% ab initio | 719 | 727 |
partial | 247 | 278 |
with major correction(s) | 358 | 376 |
known RefSeq (NP_) | 8,379 | 8,350 |
model RefSeq (XP_) | 60,304 | 59,990 |
Detailed reports
The counts below do not include pseudogenes.Feature lengths
Feature | Count | Mean length (bp) | Median length (bp) | Min length (bp) | Max length (bp) |
---|---|---|---|---|---|
Genes | 25,367 | 28,097 | 9,398 | 48 | 1,287,844 |
All transcripts | 84,794 | 4,625 | 3,506 | 17 | 107,597 |
mRNA | 68,670 | 4,649 | 3,655 | 249 | 107,597 |
misc_RNA | 4,188 | 4,709 | 3,113 | 111 | 55,142 |
miRNA | 1,209 | 22 | 22 | 17 | 40 |
tRNA | 303 | 74 | 73 | 65 | 87 |
lncRNA | 10,062 | 5,270 | 2,954 | 92 | 67,454 |
snoRNA | 186 | 108 | 92 | 62 | 321 |
snRNA | 67 | 140 | 141 | 59 | 194 |
rRNA | 94 | 1,241 | 153 | 118 | 4,446 |
telomerase_RNA | 1 | 465 | 465 | 465 | 465 |
SRP_RNA | 1 | 290 | 290 | 290 | 290 |
Single-exon transcripts | 870 | 2,064 | 1,543 | 92 | 16,651 |
coding transcripts (NM_/XM_ ) | 868 | 2,068 | 1,549 | 297 | 16,651 |
non-coding transcripts (NR_/XR_ ) | 2 | 405 | 718 | 92 | 718 |
CDSs | 68,683 | 2,202 | 1,584 | 96 | 106,392 |
Exons | 262,919 | 490 | 141 | 1 | 63,487 |
in coding transcripts (NM_/XM_ ) | 231,973 | 401 | 137 | 1 | 50,176 |
in non-coding transcripts (NR_/XR_ ) | 48,364 | 814 | 158 | 2 | 63,487 |
Introns | 241,290 | 4,145 | 927 | 30 | 983,230 |
in coding transcripts (NM_/XM_ ) | 218,234 | 3,971 | 892 | 30 | 983,230 |
in non-coding transcripts (NR_/XR_ ) | 39,798 | 4,674 | 1,112 | 30 | 374,058 |
Transcripts per gene, exons per transcript
Mean | Median | Min | Max | |
---|---|---|---|---|
Number of transcripts per gene | 3.36 | 1 | 1 | 58 |
Number of exons per transcript | 13.24 | 10 | 1 | 328 |
Feature | Count | Mean length (bp) | Median length (bp) | Min length (bp) | Max length (bp) |
---|---|---|---|---|---|
Genes | 25,306 | 28,246 | 9,497 | 48 | 1,287,842 |
All transcripts | 84,476 | 4,702 | 3,553 | 17 | 107,267 |
mRNA | 68,341 | 4,712 | 3,696 | 216 | 107,267 |
misc_RNA | 4,302 | 5,051 | 3,326 | 127 | 55,142 |
miRNA | 1,215 | 22 | 22 | 17 | 28 |
tRNA | 267 | 74 | 73 | 71 | 87 |
lncRNA | 9,973 | 5,343 | 3,080 | 92 | 63,863 |
snoRNA | 188 | 107 | 92 | 62 | 321 |
snRNA | 75 | 141 | 141 | 59 | 194 |
rRNA | 100 | 587 | 119 | 118 | 4,459 |
telomerase_RNA | 1 | 465 | 465 | 465 | 465 |
SRP_RNA | 1 | 290 | 290 | 290 | 290 |
Single-exon transcripts | 891 | 2,082 | 1,421 | 92 | 22,476 |
coding transcripts (NM_/XM_ ) | 889 | 2,086 | 1,423 | 297 | 22,476 |
non-coding transcripts (NR_/XR_ ) | 2 | 405 | 718 | 92 | 718 |
CDSs | 68,341 | 2,209 | 1,593 | 96 | 106,062 |
Exons | 261,993 | 500 | 141 | 1 | 56,844 |
in coding transcripts (NM_/XM_ ) | 231,029 | 406 | 137 | 1 | 51,979 |
in non-coding transcripts (NR_/XR_ ) | 48,708 | 839 | 159 | 2 | 56,844 |
Introns | 240,366 | 4,158 | 932 | 25 | 1,068,968 |
in coding transcripts (NM_/XM_ ) | 217,331 | 3,987 | 896 | 25 | 1,068,968 |
in non-coding transcripts (NR_/XR_ ) | 40,067 | 4,613 | 1,117 | 31 | 373,054 |
Transcripts per gene, exons per transcript
Mean | Median | Min | Max | |
---|---|---|---|---|
Number of transcripts per gene | 3.34 | 1 | 1 | 58 |
Number of exons per transcript | 13.31 | 10 | 1 | 324 |
BUSCO analysis of gene annotation
BUSCO v4.1.4 was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the aves_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation.
Alignment of the annotated proteins to a set of high-quality proteins
The final set of annotated proteins was searched with BLASTP against the UniProtKB/Swiss-Prot curated proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 18010 coding genes, 16591 genes had a protein with an alignment covering 50% or more of the query and 11471 had an alignment covering 95% or more of the query.Definition of query and target coverage. The query coverage is the percentage of the annotated protein length that is included in the alignment. The target coverage is the percentage of the target length that is included in the alignment.
Below is a cumulative graph displaying the number of genes with alignments above a given query or target coverage threshold. For comparison, corresponding statistics for other organisms annotated by the NCBI eukaryotic annotation pipeline were added to the graph.
Query: annotated proteinsTarget: UniProtKB/Swiss-Prot curated proteins
Masking of genomic sequence
Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker (if calculated), for each assembly. RepeatMasker results are only calculated for organisms with complete Dfam HMM model collections.
For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.Assembly name | Assembly accession | % Masked with WindowMasker |
---|---|---|
bGalGal1.mat.broiler.GRCg7b | GCF_016699485.2 | 20.54% |
bGalGal1.pat.whiteleghornlayer.GRCg7w | GCF_016700215.2 | 20.22% |
Transcript and protein alignments
The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign, minimap2, or ProSplign and passed to Gnomon, NCBI's gene prediction software.
Transcript alignments
Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by Splign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|
Same-species known RefSeq (NM_/NR_) | 9,470 | 9,375 (99.00%) | 9,315 (98.36%) | 99.95% | 99.93% |
Same-species Genbank | 30,935 | 30,224 (97.70%) | 27,628 (89.31%) | 99.42% | 98.81% |
Same-species EST | 826,890 | 733,914 (88.76%) | 656,374 (79.38%) | 98.74% | 98.72% |
Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by Splign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|
Same-species known RefSeq (NM_/NR_) | 9,470 | 9,339 (98.62%) | 9,281 (98.00%) | 99.64% | 99.87% |
Same-species Genbank | 30,935 | 30,213 (97.67%) | 27,563 (89.10%) | 99.49% | 99.01% |
Same-species EST | 826,890 | 734,231 (88.79%) | 657,919 (79.57%) | 98.78% | 98.74% |
RefSeq transcript alignment quality report
The known RefSeq transcripts (NM_ and NR_ accessions) are a set of hiqh-quality transcripts maintained by the RefSeq group at NCBI. Alignment statistics for this group of transcripts, such as percent and number of sequences not aligning at all, percent best alignments split between multiple scaffolds, and percent alignments not covering the full CDS are indicative of the genome quality and are provided below.
bGalGal1.mat.broiler.GRCg7b Primary Assembly | bGalGal1.pat.whiteleghornlayer.GRCg7w Primary Assembly | |
---|---|---|
Number of sequences retrieved from Entrez | 9,470 | 9,470 |
Number (%) of sequences not aligning | 95 (1.00%) | 131 (1.38%) |
Number (%) of sequences with multiple best alignments (split genes) | 1 (0.01%) | 6 (0.06%) |
Number (%) of sequences with CDS coverage < 95% | 28 (0.33%) | 45 (0.54%) |
RNA-Seq alignments
The following RNA-Seq reads from the Sequence Read Archive were also used for gene prediction:
Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)Sample Id | Publication | Track name | Number of reads | Percent aligned reads | Percent of aligned reads with introns | Number of introns |
---|---|---|---|---|---|---|
All | NA | Aggregate of all aligned samples | 11,211,076,167 | 80% | 32% | 304,652 |
SAMEA103992290 | NA | testis (Gallus gallus, SAMEA103992290) | 220,585,760 | 87% | 40% | 248,465 |
SAMEA103992323 | NA | ileum (Gallus gallus, SAMEA103992323) | 244,196,352 | 87% | 34% | 215,903 |
SAMEA103992393 | NA | cerebellum (Gallus gallus, SAMEA103992393) | 197,633,632 | 82% | 26% | 212,695 |
SAMEA103992415 | NA | pectoral muscle (Gallus gallus, SAMEA103992415) | 212,270,152 | 81% | 48% | 180,105 |
SAMEA103992428 | NA | kidney (Gallus gallus, SAMEA103992428) | 164,194,408 | 80% | 35% | 204,591 |
SAMEA103992432 | NA | gizzard (Gallus gallus, SAMEA103992432) | 210,801,006 | 85% | 37% | 201,455 |
SAMEA103992437 | NA | pectoral muscle (Gallus gallus, SAMEA103992437) | 214,118,912 | 80% | 46% | 176,950 |
SAMEA103992440 | NA | gizzard (Gallus gallus, SAMEA103992440) | 222,225,634 | 82% | 37% | 203,331 |
SAMEA103992453 | NA | gizzard (Gallus gallus, SAMEA103992453) | 201,296,672 | 84% | 38% | 193,829 |
SAMEA103992470 | NA | pectoral muscle (Gallus gallus, SAMEA103992470) | 223,862,922 | 81% | 50% | 177,272 |
SAMEA103992482 | NA | cerebellum (Gallus gallus, SAMEA103992482) | 222,342,158 | 81% | 26% | 215,161 |
SAMEA103992484 | NA | duodenum (Gallus gallus, SAMEA103992484) | 263,365,874 | 79% | 36% | 218,759 |
SAMEA103992527 | NA | lung parenchyma (Gallus gallus, SAMEA103992527) | 158,913,204 | 82% | 29% | 208,790 |
SAMEA103992528 | NA | cerebellum (Gallus gallus, SAMEA103992528) | 196,347,632 | 83% | 26% | 211,728 |
SAMEA103992531 | NA | duodenum (Gallus gallus, SAMEA103992531) | 239,824,454 | 80% | 34% | 219,398 |
SAMEA103992533 | NA | cerebellum (Gallus gallus, SAMEA103992533) | 256,786,654 | 82% | 26% | 214,820 |
SAMEA103992543 | NA | gizzard (Gallus gallus, SAMEA103992543) | 198,011,362 | 84% | 36% | 197,772 |
SAMEA103992544 | NA | duodenum (Gallus gallus, SAMEA103992544) | 175,054,892 | 79% | 32% | 214,798 |
SAMEA103992559 | NA | kidney (Gallus gallus, SAMEA103992559) | 209,883,026 | 80% | 35% | 214,308 |
SAMEA103992570 | NA | pectoral muscle (Gallus gallus, SAMEA103992570) | 217,238,362 | 84% | 48% | 172,387 |
SAMEA103992604 | NA | kidney (Gallus gallus, SAMEA103992604) | 225,777,268 | 79% | 33% | 220,266 |
SAMEA103992623 | NA | kidney (Gallus gallus, SAMEA103992623) | 202,398,932 | 77% | 32% | 214,304 |
SAMEA103992639 | NA | ileum (Gallus gallus, SAMEA103992639) | 201,299,902 | 85% | 36% | 212,625 |
SAMEA103992648 | NA | lung parenchyma (Gallus gallus, SAMEA103992648) | 154,510,862 | 85% | 29% | 204,789 |
SAMEA103992660 | NA | lung parenchyma (Gallus gallus, SAMEA103992660) | 175,258,270 | 77% | 30% | 200,904 |
SAMEA103992683 | NA | ileum (Gallus gallus, SAMEA103992683) | 175,482,096 | 83% | 34% | 211,851 |
SAMEA103992692 | NA | ileum (Gallus gallus, SAMEA103992692) | 223,396,454 | 83% | 33% | 216,799 |
SAMEA2812691 | NA | heterophil, LPS (Gallus gallus, SAMEA2812691) | 31,262,328 | 87% | 27% | 130,011 |
SAMEA2812692 | NA | macrophage, LPS (Gallus gallus, SAMEA2812692) | 28,221,016 | 81% | 28% | 120,557 |
SAMEA2812693 | NA | dendritic cell, LPS (Gallus gallus, SAMEA2812693) | 27,087,284 | 84% | 25% | 125,360 |
SAMEA2812694 | NA | macrophage, control (Gallus gallus, SAMEA2812694) | 34,097,602 | 80% | 28% | 131,652 |
SAMEA2812695 | NA | heterophil, control (Gallus gallus, SAMEA2812695) | 37,317,268 | 86% | 27% | 135,881 |
SAMEA2812696 | NA | dendritic cell, control (Gallus gallus, SAMEA2812696) | 33,666,450 | 88% | 28% | 133,845 |
SAMEA3109050 | NA | bone marrow macrophage, (Gallus gallus, SAMEA3109050) | 75,174,726 | 85% | 28% | 154,737 |
SAMEA3109051 | NA | embryonic cell, (Gallus gallus, SAMEA3109051) | 149,656,536 | 84% | 25% | 210,278 |
SAMEA3109052 | NA | bone marrow macrophage, (Gallus gallus, SAMEA3109052) | 129,134,996 | 77% | 26% | 164,180 |
SAMEA3109053 | NA | DF-1 cell, (Gallus gallus, SAMEA3109053) | 94,156,104 | 85% | 31% | 152,751 |
SAMN00000795 | 15592404,20622855,28135246,23211792 | Gallus gallus; red junglefowl RJF #256 (Gallus gallus, female, SAMN00000795) | 910,887 | 78% | 17% | 45,832 |
SAMN02738215 | 25152353 | regenerating early grow body contour feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738215) | 189,244,660 | 85% | 14% | 137,275 |
SAMN02738216 | 25152353 | regenerating early grow body contour feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738216) | 120,570,422 | 82% | 20% | 154,774 |
SAMN02738217 | 25152353 | regenerating early grow body contour feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738217) | 106,499,126 | 84% | 22% | 162,741 |
SAMN02738218 | 25152353 | regenerating late grow body contour feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738218) | 146,181,954 | 87% | 24% | 174,591 |
SAMN02738219 | 25152353 | regenerating late grow body contour feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738219) | 148,599,532 | 87% | 20% | 167,977 |
SAMN02738220 | 25152353 | regenerating late grow body contour feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738220) | 106,842,912 | 87% | 20% | 166,150 |
SAMN02738221 | 25152353 | regenerating early grow wing flight feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738221) | 143,622,554 | 84% | 25% | 180,867 |
SAMN02738222 | 25152353 | regenerating early grow wing flight feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738222) | 145,335,050 | 86% | 25% | 175,317 |
SAMN02738223 | 25152353 | regenerating early grow wing flight feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738223) | 118,280,422 | 86% | 25% | 176,211 |
SAMN02738224 | 25152353 | regenerating middle grow wing flight feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738224) | 156,832,008 | 86% | 18% | 179,224 |
SAMN02738225 | 25152353 | regenerating middle grow wing flight feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738225) | 150,783,768 | 86% | 18% | 175,673 |
SAMN02738226 | 25152353 | regenerating middle grow wing flight feather (replicate 3) (Gallus gallus, 2yr, Male, SAMN02738226) | 152,273,494 | 86% | 18% | 172,566 |
SAMN02738227 | 25152353 | regenerating late grow wing flight feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738227) | 142,016,780 | 87% | 22% | 169,997 |
SAMN02738228 | 25152353 | regenerating late grow wing flight feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738228) | 113,006,108 | 87% | 20% | 158,478 |
SAMN02738229 | 25152353 | regenerating late grow wing flight feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738229) | 146,813,926 | 87% | 21% | 170,718 |
SAMN02979340 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979340) | 4,239,440 | 53% | 31% | 93,099 |
SAMN02979341 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979341) | 4,117,852 | 55% | 35% | 95,126 |
SAMN02979342 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979342) | 4,175,736 | 53% | 34% | 94,636 |
SAMN02979343 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979343) | 3,974,614 | 51% | 32% | 90,622 |
SAMN02979344 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979344) | 3,952,612 | 53% | 33% | 93,101 |
SAMN02979345 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979345) | 3,664,098 | 54% | 31% | 88,927 |
SAMN03376183 | NA | duodenum, low residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376183) | 80,258,102 | 71% | 25% | 165,772 |
SAMN03376184 | NA | duodenum, low residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376184) | 86,305,796 | 67% | 23% | 156,008 |
SAMN03376185 | NA | duodenum, low residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376185) | 101,028,434 | 70% | 24% | 155,523 |
SAMN03376186 | NA | duodenum, high residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376186) | 81,602,282 | 60% | 23% | 153,717 |
SAMN03376187 | NA | duodenum, high residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376187) | 88,785,322 | 60% | 24% | 160,418 |
SAMN03376188 | NA | duodenum, high residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376188) | 75,829,126 | 77% | 26% | 167,986 |
SAMN03579563 | NA | white skin (Gallus gallus, 16 week, female, SAMN03579563) | 55,400,490 | 84% | 28% | 174,779 |
SAMN03579564 | NA | black skin (Gallus gallus, 16 week, female, SAMN03579564) | 59,205,048 | 83% | 27% | 180,453 |
SAMN04013381 | 26366565 | Recessive White Rocks, high body weight (Gallus gallus, 7 Weeks, SAMN04013381) | 56,670,724 | 79% | 37% | 163,386 |
SAMN04013382 | 26366565 | Recessive White Rocks, low body weight (Gallus gallus, 7 Weeks, SAMN04013382) | 47,368,088 | 79% | 37% | 162,791 |
SAMN04013383 | 26366565 | Xing Hua Chicken, high body weight (Gallus gallus, 7 Weeks, SAMN04013383) | 50,901,084 | 74% | 38% | 151,031 |
SAMN04013384 | 26366565 | Xing Hua Chicken, low body weight (Gallus gallus, 7 Weeks, SAMN04013384) | 90,471,262 | 73% | 36% | 163,843 |
SAMN05341171 | NA | cochlea (Gallus gallus, Ph8-11d, pooled male and female, SAMN05341171) | 151,314,258 | 82% | 32% | 212,149 |
SAMN06140852 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140852) | 175,648,792 | 82% | 33% | 206,969 |
SAMN06140853 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140853) | 153,389,158 | 81% | 39% | 216,851 |
SAMN06140854 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140854) | 162,146,116 | 83% | 34% | 203,125 |
SAMN06140855 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140855) | 158,528,308 | 81% | 39% | 204,148 |
SAMN06143075 | 28301039 | Clone 18 rep2 (Gallus gallus, SAMN06143075) | 48,534,572 | 71% | 34% | 125,046 |
SAMN06143076 | 28301039 | Clone 18 rep1 (Gallus gallus, SAMN06143076) | 72,387,134 | 70% | 33% | 126,886 |
SAMN06143077 | 28301039 | Bach2KO rep3 (Gallus gallus, SAMN06143077) | 69,547,304 | 70% | 34% | 125,435 |
SAMN06143078 | 28301039 | Bach2KO rep2 (Gallus gallus, SAMN06143078) | 69,487,136 | 67% | 33% | 123,071 |
SAMN06143079 | 28301039 | Bach2KO rep1 (Gallus gallus, SAMN06143079) | 60,446,870 | 57% | 33% | 111,257 |
SAMN06143080 | 28301039 | Clone 18 rep3 (Gallus gallus, SAMN06143080) | 31,315,162 | 70% | 34% | 118,308 |
SAMN08016552 | NA | 48 h infected-3 (Gallus gallus, SAMN08016552) | 40,664,148 | 15% | 42% | 139,228 |
SAMN08016553 | NA | 48 h infected-2 (Gallus gallus, SAMN08016553) | 47,362,010 | 14% | 45% | 143,718 |
SAMN08016554 | NA | 48 h infected-1 (Gallus gallus, SAMN08016554) | 49,530,088 | 17% | 42% | 148,509 |
SAMN08016555 | NA | 24 h infected-3 (Gallus gallus, SAMN08016555) | 46,996,798 | 42% | 43% | 172,398 |
SAMN08016556 | NA | 24 h infected-2 (Gallus gallus, SAMN08016556) | 53,546,936 | 39% | 44% | 172,727 |
SAMN08016557 | NA | 24 h infected-1 (Gallus gallus, SAMN08016557) | 45,849,362 | 41% | 43% | 170,245 |
SAMN08016558 | NA | 12 h infected-3 (Gallus gallus, SAMN08016558) | 38,018,334 | 73% | 43% | 181,381 |
SAMN08016559 | NA | 12 h infected-2 (Gallus gallus, SAMN08016559) | 37,479,300 | 75% | 43% | 180,186 |
SAMN08016560 | NA | 12 h infected-1 (Gallus gallus, SAMN08016560) | 38,934,814 | 73% | 45% | 179,432 |
SAMN08016663 | NA | 48 h mock-3 (Gallus gallus, SAMN08016663) | 48,413,434 | 82% | 44% | 179,018 |
SAMN08016664 | NA | 48 h mock-2 (Gallus gallus, SAMN08016664) | 46,740,100 | 82% | 43% | 178,991 |
SAMN08016665 | NA | 48 h mock-1 (Gallus gallus, SAMN08016665) | 44,523,570 | 81% | 43% | 178,156 |
SAMN08016666 | NA | 24 h mock-3 (Gallus gallus, SAMN08016666) | 48,588,828 | 82% | 41% | 180,428 |
SAMN08016667 | NA | 24 h mock-2 (Gallus gallus, SAMN08016667) | 49,375,266 | 82% | 44% | 180,936 |
SAMN08016668 | NA | 24 h mock-1 (Gallus gallus, SAMN08016668) | 49,023,726 | 82% | 42% | 180,489 |
SAMN08016669 | NA | 12 h mock-3 (Gallus gallus, SAMN08016669) | 35,866,470 | 82% | 41% | 178,451 |
SAMN08016670 | NA | 12 h mock-2 (Gallus gallus, SAMN08016670) | 49,919,738 | 82% | 42% | 185,418 |
SAMN08016671 | NA | 12 h mock-1 (Gallus gallus, SAMN08016671) | 54,883,560 | 82% | 42% | 186,971 |
Sample Id | Publication | Track name | Number of reads | Percent aligned reads | Percent of aligned reads with introns | Number of introns |
---|---|---|---|---|---|---|
All | NA | Aggregate of all aligned samples | 11,211,076,167 | 80% | 32% | 302,505 |
SAMEA103992290 | NA | testis (Gallus gallus, SAMEA103992290) | 220,585,760 | 87% | 40% | 247,662 |
SAMEA103992323 | NA | ileum (Gallus gallus, SAMEA103992323) | 244,196,352 | 87% | 34% | 214,066 |
SAMEA103992393 | NA | cerebellum (Gallus gallus, SAMEA103992393) | 197,633,632 | 83% | 26% | 211,502 |
SAMEA103992415 | NA | pectoral muscle (Gallus gallus, SAMEA103992415) | 212,270,152 | 80% | 47% | 178,416 |
SAMEA103992428 | NA | kidney (Gallus gallus, SAMEA103992428) | 164,194,408 | 81% | 35% | 203,351 |
SAMEA103992432 | NA | gizzard (Gallus gallus, SAMEA103992432) | 210,801,006 | 85% | 37% | 199,552 |
SAMEA103992437 | NA | pectoral muscle (Gallus gallus, SAMEA103992437) | 214,118,912 | 80% | 46% | 175,532 |
SAMEA103992440 | NA | gizzard (Gallus gallus, SAMEA103992440) | 222,225,634 | 83% | 37% | 201,965 |
SAMEA103992453 | NA | gizzard (Gallus gallus, SAMEA103992453) | 201,296,672 | 84% | 38% | 192,122 |
SAMEA103992470 | NA | pectoral muscle (Gallus gallus, SAMEA103992470) | 223,862,922 | 81% | 50% | 176,205 |
SAMEA103992482 | NA | cerebellum (Gallus gallus, SAMEA103992482) | 222,342,158 | 81% | 26% | 213,552 |
SAMEA103992484 | NA | duodenum (Gallus gallus, SAMEA103992484) | 263,365,874 | 79% | 36% | 217,089 |
SAMEA103992527 | NA | lung parenchyma (Gallus gallus, SAMEA103992527) | 158,913,204 | 82% | 29% | 207,225 |
SAMEA103992528 | NA | cerebellum (Gallus gallus, SAMEA103992528) | 196,347,632 | 83% | 26% | 210,239 |
SAMEA103992531 | NA | duodenum (Gallus gallus, SAMEA103992531) | 239,824,454 | 80% | 33% | 217,076 |
SAMEA103992533 | NA | cerebellum (Gallus gallus, SAMEA103992533) | 256,786,654 | 83% | 26% | 213,542 |
SAMEA103992543 | NA | gizzard (Gallus gallus, SAMEA103992543) | 198,011,362 | 84% | 36% | 196,370 |
SAMEA103992544 | NA | duodenum (Gallus gallus, SAMEA103992544) | 175,054,892 | 80% | 31% | 212,525 |
SAMEA103992559 | NA | kidney (Gallus gallus, SAMEA103992559) | 209,883,026 | 80% | 35% | 213,133 |
SAMEA103992570 | NA | pectoral muscle (Gallus gallus, SAMEA103992570) | 217,238,362 | 84% | 48% | 171,370 |
SAMEA103992604 | NA | kidney (Gallus gallus, SAMEA103992604) | 225,777,268 | 80% | 33% | 218,454 |
SAMEA103992623 | NA | kidney (Gallus gallus, SAMEA103992623) | 202,398,932 | 77% | 32% | 212,623 |
SAMEA103992639 | NA | ileum (Gallus gallus, SAMEA103992639) | 201,299,902 | 85% | 36% | 210,974 |
SAMEA103992648 | NA | lung parenchyma (Gallus gallus, SAMEA103992648) | 154,510,862 | 85% | 29% | 202,754 |
SAMEA103992660 | NA | lung parenchyma (Gallus gallus, SAMEA103992660) | 175,258,270 | 77% | 30% | 199,505 |
SAMEA103992683 | NA | ileum (Gallus gallus, SAMEA103992683) | 175,482,096 | 84% | 34% | 209,788 |
SAMEA103992692 | NA | ileum (Gallus gallus, SAMEA103992692) | 223,396,454 | 84% | 33% | 214,557 |
SAMEA2812691 | NA | heterophil, LPS (Gallus gallus, SAMEA2812691) | 31,262,328 | 85% | 27% | 128,184 |
SAMEA2812692 | NA | macrophage, LPS (Gallus gallus, SAMEA2812692) | 28,221,016 | 81% | 28% | 119,511 |
SAMEA2812693 | NA | dendritic cell, LPS (Gallus gallus, SAMEA2812693) | 27,087,284 | 84% | 24% | 124,217 |
SAMEA2812694 | NA | macrophage, control (Gallus gallus, SAMEA2812694) | 34,097,602 | 80% | 28% | 130,567 |
SAMEA2812695 | NA | heterophil, control (Gallus gallus, SAMEA2812695) | 37,317,268 | 85% | 27% | 133,974 |
SAMEA2812696 | NA | dendritic cell, control (Gallus gallus, SAMEA2812696) | 33,666,450 | 88% | 28% | 132,733 |
SAMEA3109050 | NA | bone marrow macrophage, (Gallus gallus, SAMEA3109050) | 75,174,726 | 85% | 28% | 153,114 |
SAMEA3109051 | NA | embryonic cell, (Gallus gallus, SAMEA3109051) | 149,656,536 | 84% | 25% | 208,208 |
SAMEA3109052 | NA | bone marrow macrophage, (Gallus gallus, SAMEA3109052) | 129,134,996 | 77% | 26% | 162,456 |
SAMEA3109053 | NA | DF-1 cell, (Gallus gallus, SAMEA3109053) | 94,156,104 | 84% | 31% | 151,262 |
SAMN00000795 | 15592404,20622855,28135246,23211792 | Gallus gallus; red junglefowl RJF #256 (Gallus gallus, female, SAMN00000795) | 910,887 | 79% | 17% | 45,955 |
SAMN02738215 | 25152353 | regenerating early grow body contour feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738215) | 189,244,660 | 86% | 14% | 135,959 |
SAMN02738216 | 25152353 | regenerating early grow body contour feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738216) | 120,570,422 | 84% | 20% | 153,126 |
SAMN02738217 | 25152353 | regenerating early grow body contour feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738217) | 106,499,126 | 85% | 22% | 160,922 |
SAMN02738218 | 25152353 | regenerating late grow body contour feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738218) | 146,181,954 | 87% | 24% | 172,719 |
SAMN02738219 | 25152353 | regenerating late grow body contour feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738219) | 148,599,532 | 87% | 20% | 166,049 |
SAMN02738220 | 25152353 | regenerating late grow body contour feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738220) | 106,842,912 | 87% | 20% | 164,436 |
SAMN02738221 | 25152353 | regenerating early grow wing flight feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738221) | 143,622,554 | 86% | 25% | 179,018 |
SAMN02738222 | 25152353 | regenerating early grow wing flight feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738222) | 145,335,050 | 87% | 24% | 173,375 |
SAMN02738223 | 25152353 | regenerating early grow wing flight feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738223) | 118,280,422 | 86% | 25% | 174,300 |
SAMN02738224 | 25152353 | regenerating middle grow wing flight feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738224) | 156,832,008 | 86% | 18% | 177,360 |
SAMN02738225 | 25152353 | regenerating middle grow wing flight feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738225) | 150,783,768 | 87% | 18% | 173,705 |
SAMN02738226 | 25152353 | regenerating middle grow wing flight feather (replicate 3) (Gallus gallus, 2yr, Male, SAMN02738226) | 152,273,494 | 86% | 18% | 170,607 |
SAMN02738227 | 25152353 | regenerating late grow wing flight feather epithelium (replicate 1) (Gallus gallus, 2yr, male, SAMN02738227) | 142,016,780 | 87% | 22% | 167,983 |
SAMN02738228 | 25152353 | regenerating late grow wing flight feather epithelium (replicate 2) (Gallus gallus, 2yr, male, SAMN02738228) | 113,006,108 | 85% | 21% | 156,597 |
SAMN02738229 | 25152353 | regenerating late grow wing flight feather epithelium (replicate 3) (Gallus gallus, 2yr, male, SAMN02738229) | 146,813,926 | 86% | 22% | 168,698 |
SAMN02979340 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979340) | 4,239,440 | 53% | 31% | 92,243 |
SAMN02979341 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979341) | 4,117,852 | 55% | 34% | 94,150 |
SAMN02979342 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979342) | 4,175,736 | 53% | 33% | 93,719 |
SAMN02979343 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979343) | 3,974,614 | 50% | 31% | 89,660 |
SAMN02979344 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979344) | 3,952,612 | 53% | 33% | 92,401 |
SAMN02979345 | 26053856 | embryonic fibroblast cell line, (Gallus gallus, SAMN02979345) | 3,664,098 | 54% | 30% | 88,045 |
SAMN03376183 | NA | duodenum, low residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376183) | 80,258,102 | 71% | 26% | 163,746 |
SAMN03376184 | NA | duodenum, low residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376184) | 86,305,796 | 67% | 23% | 154,222 |
SAMN03376185 | NA | duodenum, low residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376185) | 101,028,434 | 71% | 24% | 153,649 |
SAMN03376186 | NA | duodenum, high residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376186) | 81,602,282 | 60% | 23% | 152,174 |
SAMN03376187 | NA | duodenum, high residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376187) | 88,785,322 | 61% | 24% | 158,770 |
SAMN03376188 | NA | duodenum, high residual feed intake (Gallus gallus, 61 weeks of age, female, SAMN03376188) | 75,829,126 | 77% | 26% | 166,253 |
SAMN03579563 | NA | white skin (Gallus gallus, 16 week, female, SAMN03579563) | 55,400,490 | 83% | 27% | 172,799 |
SAMN03579564 | NA | black skin (Gallus gallus, 16 week, female, SAMN03579564) | 59,205,048 | 82% | 26% | 178,321 |
SAMN04013381 | 26366565 | Recessive White Rocks, high body weight (Gallus gallus, 7 Weeks, SAMN04013381) | 56,670,724 | 78% | 36% | 161,574 |
SAMN04013382 | 26366565 | Recessive White Rocks, low body weight (Gallus gallus, 7 Weeks, SAMN04013382) | 47,368,088 | 78% | 36% | 160,850 |
SAMN04013383 | 26366565 | Xing Hua Chicken, high body weight (Gallus gallus, 7 Weeks, SAMN04013383) | 50,901,084 | 72% | 37% | 149,230 |
SAMN04013384 | 26366565 | Xing Hua Chicken, low body weight (Gallus gallus, 7 Weeks, SAMN04013384) | 90,471,262 | 72% | 36% | 162,012 |
SAMN05341171 | NA | cochlea (Gallus gallus, Ph8-11d, pooled male and female, SAMN05341171) | 151,314,258 | 82% | 32% | 210,025 |
SAMN06140852 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140852) | 175,648,792 | 82% | 33% | 204,243 |
SAMN06140853 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140853) | 153,389,158 | 81% | 38% | 214,287 |
SAMN06140854 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140854) | 162,146,116 | 83% | 33% | 200,593 |
SAMN06140855 | NA | Thyroid gland (Gallus gallus, 39 weeks, female, SAMN06140855) | 158,528,308 | 81% | 39% | 201,886 |
SAMN06143075 | 28301039 | Clone 18 rep2 (Gallus gallus, SAMN06143075) | 48,534,572 | 72% | 33% | 123,959 |
SAMN06143076 | 28301039 | Clone 18 rep1 (Gallus gallus, SAMN06143076) | 72,387,134 | 71% | 33% | 125,761 |
SAMN06143077 | 28301039 | Bach2KO rep3 (Gallus gallus, SAMN06143077) | 69,547,304 | 70% | 34% | 124,383 |
SAMN06143078 | 28301039 | Bach2KO rep2 (Gallus gallus, SAMN06143078) | 69,487,136 | 67% | 33% | 122,126 |
SAMN06143079 | 28301039 | Bach2KO rep1 (Gallus gallus, SAMN06143079) | 60,446,870 | 58% | 32% | 110,308 |
SAMN06143080 | 28301039 | Clone 18 rep3 (Gallus gallus, SAMN06143080) | 31,315,162 | 71% | 34% | 117,288 |
SAMN08016552 | NA | 48 h infected-3 (Gallus gallus, SAMN08016552) | 40,664,148 | 15% | 42% | 138,083 |
SAMN08016553 | NA | 48 h infected-2 (Gallus gallus, SAMN08016553) | 47,362,010 | 14% | 44% | 142,574 |
SAMN08016554 | NA | 48 h infected-1 (Gallus gallus, SAMN08016554) | 49,530,088 | 17% | 42% | 147,520 |
SAMN08016555 | NA | 24 h infected-3 (Gallus gallus, SAMN08016555) | 46,996,798 | 41% | 43% | 171,225 |
SAMN08016556 | NA | 24 h infected-2 (Gallus gallus, SAMN08016556) | 53,546,936 | 39% | 44% | 171,427 |
SAMN08016557 | NA | 24 h infected-1 (Gallus gallus, SAMN08016557) | 45,849,362 | 41% | 43% | 169,037 |
SAMN08016558 | NA | 12 h infected-3 (Gallus gallus, SAMN08016558) | 38,018,334 | 73% | 43% | 180,325 |
SAMN08016559 | NA | 12 h infected-2 (Gallus gallus, SAMN08016559) | 37,479,300 | 75% | 43% | 179,000 |
SAMN08016560 | NA | 12 h infected-1 (Gallus gallus, SAMN08016560) | 38,934,814 | 72% | 45% | 178,161 |
SAMN08016663 | NA | 48 h mock-3 (Gallus gallus, SAMN08016663) | 48,413,434 | 82% | 44% | 178,023 |
SAMN08016664 | NA | 48 h mock-2 (Gallus gallus, SAMN08016664) | 46,740,100 | 82% | 42% | 177,908 |
SAMN08016665 | NA | 48 h mock-1 (Gallus gallus, SAMN08016665) | 44,523,570 | 81% | 43% | 177,141 |
SAMN08016666 | NA | 24 h mock-3 (Gallus gallus, SAMN08016666) | 48,588,828 | 82% | 41% | 179,454 |
SAMN08016667 | NA | 24 h mock-2 (Gallus gallus, SAMN08016667) | 49,375,266 | 82% | 43% | 179,879 |
SAMN08016668 | NA | 24 h mock-1 (Gallus gallus, SAMN08016668) | 49,023,726 | 82% | 42% | 179,579 |
SAMN08016669 | NA | 12 h mock-3 (Gallus gallus, SAMN08016669) | 35,866,470 | 82% | 41% | 177,406 |
SAMN08016670 | NA | 12 h mock-2 (Gallus gallus, SAMN08016670) | 49,919,738 | 82% | 42% | 184,503 |
SAMN08016671 | NA | 12 h mock-1 (Gallus gallus, SAMN08016671) | 54,883,560 | 82% | 42% | 185,932 |
CAGE alignments
The following CAGE reads from the Sequence Read Archive were also used for gene prediction:
Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)Sample Id | Publication | Track name | Number of reads | Percent aligned reads | Percent of aligned reads with introns |
---|---|---|---|---|---|
All | NA | Aggregate of all aligned samples | 4,126,488,131 | 33% | 29% |
SAMD00053745 | 28241135 | whole body (Gallus gallus, SAMD00053745) | 26,566,601 | 22% | 0% |
SAMD00053746 | 28241135 | whole body (Gallus gallus, SAMD00053746) | 42,149,545 | 28% | 1% |
SAMD00053747 | 28241135 | whole body (Gallus gallus, SAMD00053747) | 39,444,330 | ||
SAMD00053748 | 28241135 | whole body (Gallus gallus, SAMD00053748) | 45,992,300 | ||
SAMD00053749 | 28241135 | whole body (Gallus gallus, SAMD00053749) | 44,790,545 | 12% | 0% |
SAMD00053750 | 28241135 | whole body (Gallus gallus, SAMD00053750) | 41,139,783 | ||
SAMD00053751 | 28241135 | whole body (Gallus gallus, SAMD00053751) | 41,058,111 | 30% | 1% |
SAMD00053752 | 28241135 | whole body (Gallus gallus, SAMD00053752) | 26,700,668 | ||
SAMD00053753 | 28241135 | whole body (Gallus gallus, SAMD00053753) | 20,686,763 | 28% | 0% |
SAMD00053754 | 28241135 | whole body (Gallus gallus, SAMD00053754) | 24,024,988 | ||
SAMD00053755 | 28241135 | whole body (Gallus gallus, SAMD00053755) | 19,614,860 | 30% | 0% |
SAMD00053756 | 28241135 | whole body (Gallus gallus, SAMD00053756) | 19,243,915 | ||
SAMD00053757 | 28241135 | whole body (Gallus gallus, SAMD00053757) | 21,309,335 | 30% | 0% |
SAMD00053758 | 28241135 | whole body (Gallus gallus, SAMD00053758) | 23,821,909 | ||
SAMD00053759 | 28241135 | whole body (Gallus gallus, SAMD00053759) | 25,827,553 | 31% | 0% |
SAMD00053760 | 28241135 | whole body (Gallus gallus, SAMD00053760) | 12,598,106 | ||
SAMD00053761 | 28241135 | whole body (Gallus gallus, SAMD00053761) | 22,609,539 | 32% | 0% |
SAMD00053762 | 28241135 | whole body (Gallus gallus, SAMD00053762) | 20,415,757 | ||
SAMD00053763 | 28241135 | whole body (Gallus gallus, SAMD00053763) | 22,315,378 | 26% | 0% |
SAMD00053764 | 28241135 | whole body (Gallus gallus, SAMD00053764) | 17,216,096 | ||
SAMD00053765 | 28241135 | whole body (Gallus gallus, SAMD00053765) | 23,850,963 | ||
SAMD00053766 | 28241135 | extraembryonic tissue (Gallus gallus, SAMD00053766) | 22,834,933 | 34% | 0% |
SAMD00053767 | 28241135 | extraembryonic tissue (Gallus gallus, SAMD00053767) | 8,643,356 | ||
SAMD00053768 | 28241135 | wing bud (Gallus gallus, SAMD00053768) | 13,206,851 | ||
SAMD00053769 | 28241135 | leg bud (Gallus gallus, SAMD00053769) | 30,634,474 | 31% | 0% |
SAMD00053770 | 28241135 | whole body (Gallus gallus, SAMD00053770) | 19,133,719 | ||
SAMD00053771 | 28241135 | hepatocyte, (Gallus gallus, female, SAMD00053771) | 14,224,248 | 22% | 0% |
SAMD00053772 | 28241135 | bone marrow, mesenchymal stem cell, (Gallus gallus, female, SAMD00053772) | 27,832,375 | 27% | 0% |
SAMD00053773 | 28241135 | aortic smooth muscle cell, (Gallus gallus, SAMD00053773) | 30,042,564 | 27% | 0% |
SAMD00053774 | 28241135 | hepatocyte, (Gallus gallus, female, SAMD00053774) | 28,828,623 | 24% | 0% |
SAMD00053775 | 28241135 | aortic smooth muscle cell, (Gallus gallus, SAMD00053775) | 24,027,393 | 25% | 0% |
SAMD00053776 | 28241135 | aortic smooth muscle cell, (Gallus gallus, SAMD00053776) | 31,668,632 | 25% | 0% |
SAMN16585353 | NA | Adipose (Gallus gallus, 20 weeks, female, SAMN16585353) | 22,443,136 | 34% | 31% |
SAMN16585354 | NA | Adipose (Gallus gallus, 20 weeks, female, SAMN16585354) | 26,974,814 | 38% | 30% |
SAMN16585355 | NA | Adipose (Gallus gallus, 20 weeks, male, SAMN16585355) | 33,791,758 | 36% | 31% |
SAMN16585356 | NA | Adipose (Gallus gallus, 20 weeks, male, SAMN16585356) | 25,480,154 | 36% | 22% |
SAMN16585357 | NA | BoneMarrow (Gallus gallus, 20 weeks, female, SAMN16585357) | 58,516,594 | 42% | 46% |
SAMN16585358 | NA | BrainCortex (Gallus gallus, 20 weeks, female, SAMN16585358) | 78,269,900 | 34% | 31% |
SAMN16585359 | NA | BrainCortex (Gallus gallus, 20 weeks, female, SAMN16585359) | 62,050,330 | 35% | 27% |
SAMN16585360 | NA | BrainCortex (Gallus gallus, 20 weeks, male, SAMN16585360) | 64,676,120 | 33% | 27% |
SAMN16585361 | NA | BrainCortex (Gallus gallus, 20 weeks, male, SAMN16585361) | 16,671,466 | 34% | 28% |
SAMN16585362 | NA | Cecum (Gallus gallus, 20 weeks, male, SAMN16585362) | 18,395,764 | 36% | 35% |
SAMN16585363 | NA | Cecum (Gallus gallus, 20 weeks, male, SAMN16585363) | 37,472,002 | 34% | 34% |
SAMN16585364 | NA | Cecum (Gallus gallus, 20 weeks, female, SAMN16585364) | 61,053,548 | 36% | 35% |
SAMN16585365 | NA | Cecum (Gallus gallus, 20 weeks, female, SAMN16585365) | 41,137,558 | 37% | 38% |
SAMN16585366 | NA | Cerebellum (Gallus gallus, 20 weeks, female, SAMN16585366) | 54,968,944 | 39% | 21% |
SAMN16585367 | NA | Cerebellum (Gallus gallus, 20 weeks, female, SAMN16585367) | 40,561,714 | 41% | 19% |
SAMN16585368 | NA | Cerebellum (Gallus gallus, 20 weeks, male, SAMN16585368) | 21,807,430 | 38% | 21% |
SAMN16585369 | NA | Cerebellum (Gallus gallus, 20 weeks, male, SAMN16585369) | 27,656,766 | 36% | 23% |
SAMN16585370 | NA | Colon (Gallus gallus, 20 weeks, male, SAMN16585370) | 27,835,794 | 34% | 35% |
SAMN16585371 | NA | Colon (Gallus gallus, 20 weeks, male, SAMN16585371) | 55,115,790 | 31% | 24% |
SAMN16585372 | NA | Colon (Gallus gallus, 20 weeks, female, SAMN16585372) | 51,073,418 | 38% | 33% |
SAMN16585373 | NA | Colon (Gallus gallus, 20 weeks, female, SAMN16585373) | 30,155,350 | 37% | 37% |
SAMN16585374 | NA | Duodenum (Gallus gallus, 20 weeks, male, SAMN16585374) | 34,698,652 | 33% | 32% |
SAMN16585375 | NA | Duodenum (Gallus gallus, 20 weeks, male, SAMN16585375) | 40,619,116 | 32% | 30% |
SAMN16585376 | NA | Duodenum (Gallus gallus, 20 weeks, female, SAMN16585376) | 63,564,738 | 35% | 35% |
SAMN16585377 | NA | Duodenum (Gallus gallus, 20 weeks, female, SAMN16585377) | 102,131,714 | 32% | 30% |
SAMN16585378 | NA | Esophagus (Gallus gallus, 20 weeks, male, SAMN16585378) | 77,095,956 | 29% | 19% |
SAMN16585379 | NA | Esophagus (Gallus gallus, 20 weeks, male, SAMN16585379) | 37,593,048 | 33% | 19% |
SAMN16585380 | NA | Esophagus (Gallus gallus, 20 weeks, female, SAMN16585380) | 38,109,036 | 34% | 33% |
SAMN16585381 | NA | Esophagus (Gallus gallus, 20 weeks, female, SAMN16585381) | 52,115,582 | 31% | 22% |
SAMN16585382 | NA | Gizzard (Gallus gallus, 20 weeks, male, SAMN16585382) | 16,757,788 | 36% | 41% |
SAMN16585383 | NA | Gizzard (Gallus gallus, 20 weeks, male, SAMN16585383) | 18,217,578 | 36% | 40% |
SAMN16585384 | NA | Gizzard (Gallus gallus, 20 weeks, female, SAMN16585384) | 53,548,268 | 37% | 34% |
SAMN16585385 | NA | Heart (Gallus gallus, 20 weeks, male, SAMN16585385) | 24,322,640 | 30% | 30% |
SAMN16585386 | NA | Heart (Gallus gallus, 20 weeks, male, SAMN16585386) | 49,273,650 | 34% | 30% |
SAMN16585387 | NA | Heart (Gallus gallus, 20 weeks, female, SAMN16585387) | 26,535,652 | 36% | 35% |
SAMN16585388 | NA | Heart (Gallus gallus, 20 weeks, female, SAMN16585388) | 60,240,362 | 34% | 36% |
SAMN16585389 | NA | Hypothalamus (Gallus gallus, 20 weeks, female, SAMN16585389) | 33,394,728 | 41% | 27% |
SAMN16585390 | NA | Hypothalamus (Gallus gallus, 20 weeks, female, SAMN16585390) | 46,376,888 | 39% | 30% |
SAMN16585391 | NA | Hypothalamus (Gallus gallus, 20 weeks, male, SAMN16585391) | 19,495,878 | 30% | 27% |
SAMN16585392 | NA | Hypothalamus (Gallus gallus, 20 weeks, male, SAMN16585392) | 21,740,930 | 35% | 30% |
SAMN16585393 | NA | Ileum (Gallus gallus, 20 weeks, male, SAMN16585393) | 25,887,390 | 36% | 31% |
SAMN16585394 | NA | Ileum (Gallus gallus, 20 weeks, male, SAMN16585394) | 25,224,666 | 35% | 34% |
SAMN16585395 | NA | Ileum (Gallus gallus, 20 weeks, female, SAMN16585395) | 59,968,480 | 37% | 39% |
SAMN16585396 | NA | Ileum (Gallus gallus, 20 weeks, female, SAMN16585396) | 61,442,554 | 35% | 38% |
SAMN16585397 | NA | Jejunum (Gallus gallus, 20 weeks, male, SAMN16585397) | 17,928,550 | 35% | 37% |
SAMN16585398 | NA | Jejunum (Gallus gallus, 20 weeks, male, SAMN16585398) | 23,263,806 | 33% | 28% |
SAMN16585399 | NA | Jejunum (Gallus gallus, 20 weeks, female, SAMN16585399) | 26,448,656 | 38% | 35% |
SAMN16585400 | NA | Jejunum (Gallus gallus, 20 weeks, female, SAMN16585400) | 35,446,302 | 37% | 40% |
SAMN16585401 | NA | Kidney (Gallus gallus, 20 weeks, male, SAMN16585401) | 24,156,570 | 39% | 42% |
SAMN16585402 | NA | Kidney (Gallus gallus, 20 weeks, male, SAMN16585402) | 19,008,634 | 41% | 29% |
SAMN16585403 | NA | Kidney (Gallus gallus, 20 weeks, female, SAMN16585403) | 72,730,590 | 38% | 51% |
SAMN16585404 | NA | Kidney (Gallus gallus, 20 weeks, female, SAMN16585404) | 42,822,380 | 41% | 42% |
SAMN16585405 | NA | Liver (Gallus gallus, 20 weeks, male, SAMN16585405) | 34,756,708 | 36% | 59% |
SAMN16585406 | NA | Liver (Gallus gallus, 20 weeks, female, SAMN16585406) | 29,691,748 | 38% | 40% |
SAMN16585407 | NA | Liver (Gallus gallus, 20 weeks, female, SAMN16585407) | 51,776,340 | 42% | 42% |
SAMN16585408 | NA | Liver (Gallus gallus, 20 weeks, male, SAMN16585408) | 21,355,456 | 40% | 50% |
SAMN16585409 | NA | Lung (Gallus gallus, 20 weeks, male, SAMN16585409) | 60,317,190 | 43% | 28% |
SAMN16585410 | NA | Lung (Gallus gallus, 20 weeks, male, SAMN16585410) | 29,533,382 | 41% | 28% |
SAMN16585411 | NA | Lung (Gallus gallus, 20 weeks, female, SAMN16585411) | 51,575,660 | 40% | 29% |
SAMN16585412 | NA | Lung (Gallus gallus, 20 weeks, female, SAMN16585412) | 42,261,360 | 39% | 27% |
SAMN16585413 | NA | Muscle (Gallus gallus, 20 weeks, female, SAMN16585413) | 40,545,678 | 38% | 38% |
SAMN16585414 | NA | Muscle (Gallus gallus, 20 weeks, female, SAMN16585414) | 31,871,648 | 35% | 33% |
SAMN16585415 | NA | Muscle (Gallus gallus, 20 weeks, male, SAMN16585415) | 34,883,006 | 36% | 37% |
SAMN16585416 | NA | Muscle (Gallus gallus, 20 weeks, male, SAMN16585416) | 37,371,258 | 38% | 43% |
SAMN16585417 | NA | Ovary (Gallus gallus, 20 weeks, female, SAMN16585417) | 85,695,582 | 36% | 37% |
SAMN16585418 | NA | Ovary (Gallus gallus, 20 weeks, female, SAMN16585418) | 65,562,992 | 37% | 28% |
SAMN16585419 | NA | Spleen (Gallus gallus, 20 weeks, male, SAMN16585419) | 52,708,494 | 41% | 34% |
SAMN16585420 | NA | Spleen (Gallus gallus, 20 weeks, female, SAMN16585420) | 36,746,136 | 43% | 33% |
SAMN16585421 | NA | Spleen (Gallus gallus, 20 weeks, female, SAMN16585421) | 43,966,666 | 37% | 24% |
SAMN16585422 | NA | Spleen (Gallus gallus, 20 weeks, male, SAMN16585422) | 40,936,772 | 38% | 28% |
SAMN16585423 | NA | Testis (Gallus gallus, 20 weeks, male, SAMN16585423) | 29,719,942 | 41% | 41% |
SAMN16585424 | NA | Testis (Gallus gallus, 20 weeks, male, SAMN16585424) | 34,177,708 | 36% | 35% |
SAMN16585425 | NA | Thymus (Gallus gallus, 20 weeks, male, SAMN16585425) | 111,246,204 | 43% | 36% |
SAMN16585426 | NA | Thymus (Gallus gallus, 20 weeks, male, SAMN16585426) | 30,111,064 | 40% | 29% |
SAMN16585427 | NA | Thymus (Gallus gallus, 20 weeks, female, SAMN16585427) | 15,670,588 | 39% | 20% |
SAMN16585428 | NA | Thymus (Gallus gallus, 20 weeks, female, SAMN16585428) | 72,338,028 | 37% | 33% |
SAMN16585429 | NA | Trachea (Gallus gallus, 20 weeks, male, SAMN16585429) | 60,241,030 | 41% | 18% |
SAMN16585430 | NA | Trachea (Gallus gallus, 20 weeks, male, SAMN16585430) | 42,704,146 | 41% | 15% |
Sample Id | Publication | Track name | Number of reads | Percent aligned reads | Percent of aligned reads with introns |
---|---|---|---|---|---|
All | NA | Aggregate of all aligned samples | 4,126,488,131 | 34% | 28% |
SAMD00053745 | 28241135 | whole body (Gallus gallus, SAMD00053745) | 26,566,601 | 21% | 0% |
SAMD00053746 | 28241135 | whole body (Gallus gallus, SAMD00053746) | 42,149,545 | 28% | 1% |
SAMD00053747 | 28241135 | whole body (Gallus gallus, SAMD00053747) | 39,444,330 | ||
SAMD00053748 | 28241135 | whole body (Gallus gallus, SAMD00053748) | 45,992,300 | ||
SAMD00053749 | 28241135 | whole body (Gallus gallus, SAMD00053749) | 44,790,545 | 12% | 0% |
SAMD00053750 | 28241135 | whole body (Gallus gallus, SAMD00053750) | 41,139,783 | ||
SAMD00053751 | 28241135 | whole body (Gallus gallus, SAMD00053751) | 41,058,111 | 30% | 1% |
SAMD00053752 | 28241135 | whole body (Gallus gallus, SAMD00053752) | 26,700,668 | ||
SAMD00053753 | 28241135 | whole body (Gallus gallus, SAMD00053753) | 20,686,763 | 27% | 0% |
SAMD00053754 | 28241135 | whole body (Gallus gallus, SAMD00053754) | 24,024,988 | ||
SAMD00053755 | 28241135 | whole body (Gallus gallus, SAMD00053755) | 19,614,860 | 29% | 0% |
SAMD00053756 | 28241135 | whole body (Gallus gallus, SAMD00053756) | 19,243,915 | ||
SAMD00053757 | 28241135 | whole body (Gallus gallus, SAMD00053757) | 21,309,335 | 29% | 0% |
SAMD00053758 | 28241135 | whole body (Gallus gallus, SAMD00053758) | 23,821,909 | ||
SAMD00053759 | 28241135 | whole body (Gallus gallus, SAMD00053759) | 25,827,553 | 31% | 0% |
SAMD00053760 | 28241135 | whole body (Gallus gallus, SAMD00053760) | 12,598,106 | ||
SAMD00053761 | 28241135 | whole body (Gallus gallus, SAMD00053761) | 22,609,539 | 32% | 0% |
SAMD00053762 | 28241135 | whole body (Gallus gallus, SAMD00053762) | 20,415,757 | ||
SAMD00053763 | 28241135 | whole body (Gallus gallus, SAMD00053763) | 22,315,378 | 26% | 0% |
SAMD00053764 | 28241135 | whole body (Gallus gallus, SAMD00053764) | 17,216,096 | ||
SAMD00053765 | 28241135 | whole body (Gallus gallus, SAMD00053765) | 23,850,963 | ||
SAMD00053766 | 28241135 | extraembryonic tissue (Gallus gallus, SAMD00053766) | 22,834,933 | 33% | 0% |
SAMD00053767 | 28241135 | extraembryonic tissue (Gallus gallus, SAMD00053767) | 8,643,356 | ||
SAMD00053768 | 28241135 | wing bud (Gallus gallus, SAMD00053768) | 13,206,851 | ||
SAMD00053769 | 28241135 | leg bud (Gallus gallus, SAMD00053769) | 30,634,474 | 30% | 0% |
SAMD00053770 | 28241135 | whole body (Gallus gallus, SAMD00053770) | 19,133,719 | ||
SAMD00053771 | 28241135 | hepatocyte, (Gallus gallus, female, SAMD00053771) | 14,224,248 | 21% | 0% |
SAMD00053772 | 28241135 | bone marrow, mesenchymal stem cell, (Gallus gallus, female, SAMD00053772) | 27,832,375 | 27% | 0% |
SAMD00053773 | 28241135 | aortic smooth muscle cell, (Gallus gallus, SAMD00053773) | 30,042,564 | 27% | 1% |
SAMD00053774 | 28241135 | hepatocyte, (Gallus gallus, female, SAMD00053774) | 28,828,623 | 24% | 0% |
SAMD00053775 | 28241135 | aortic smooth muscle cell, (Gallus gallus, SAMD00053775) | 24,027,393 | 24% | 0% |
SAMD00053776 | 28241135 | aortic smooth muscle cell, (Gallus gallus, SAMD00053776) | 31,668,632 | 24% | 0% |
SAMN16585353 | NA | Adipose (Gallus gallus, 20 weeks, female, SAMN16585353) | 22,443,136 | 35% | 30% |
SAMN16585354 | NA | Adipose (Gallus gallus, 20 weeks, female, SAMN16585354) | 26,974,814 | 39% | 30% |
SAMN16585355 | NA | Adipose (Gallus gallus, 20 weeks, male, SAMN16585355) | 33,791,758 | 38% | 30% |
SAMN16585356 | NA | Adipose (Gallus gallus, 20 weeks, male, SAMN16585356) | 25,480,154 | 38% | 21% |
SAMN16585357 | NA | BoneMarrow (Gallus gallus, 20 weeks, female, SAMN16585357) | 58,516,594 | 43% | 44% |
SAMN16585358 | NA | BrainCortex (Gallus gallus, 20 weeks, female, SAMN16585358) | 78,269,900 | 35% | 31% |
SAMN16585359 | NA | BrainCortex (Gallus gallus, 20 weeks, female, SAMN16585359) | 62,050,330 | 36% | 27% |
SAMN16585360 | NA | BrainCortex (Gallus gallus, 20 weeks, male, SAMN16585360) | 64,676,120 | 34% | 27% |
SAMN16585361 | NA | BrainCortex (Gallus gallus, 20 weeks, male, SAMN16585361) | 16,671,466 | 34% | 28% |
SAMN16585362 | NA | Cecum (Gallus gallus, 20 weeks, male, SAMN16585362) | 18,395,764 | 38% | 33% |
SAMN16585363 | NA | Cecum (Gallus gallus, 20 weeks, male, SAMN16585363) | 37,472,002 | 37% | 31% |
SAMN16585364 | NA | Cecum (Gallus gallus, 20 weeks, female, SAMN16585364) | 61,053,548 | 39% | 33% |
SAMN16585365 | NA | Cecum (Gallus gallus, 20 weeks, female, SAMN16585365) | 41,137,558 | 39% | 37% |
SAMN16585366 | NA | Cerebellum (Gallus gallus, 20 weeks, female, SAMN16585366) | 54,968,944 | 39% | 21% |
SAMN16585367 | NA | Cerebellum (Gallus gallus, 20 weeks, female, SAMN16585367) | 40,561,714 | 41% | 19% |
SAMN16585368 | NA | Cerebellum (Gallus gallus, 20 weeks, male, SAMN16585368) | 21,807,430 | 38% | 21% |
SAMN16585369 | NA | Cerebellum (Gallus gallus, 20 weeks, male, SAMN16585369) | 27,656,766 | 37% | 23% |
SAMN16585370 | NA | Colon (Gallus gallus, 20 weeks, male, SAMN16585370) | 27,835,794 | 38% | 32% |
SAMN16585371 | NA | Colon (Gallus gallus, 20 weeks, male, SAMN16585371) | 55,115,790 | 34% | 22% |
SAMN16585372 | NA | Colon (Gallus gallus, 20 weeks, female, SAMN16585372) | 51,073,418 | 39% | 32% |
SAMN16585373 | NA | Colon (Gallus gallus, 20 weeks, female, SAMN16585373) | 30,155,350 | 39% | 36% |
SAMN16585374 | NA | Duodenum (Gallus gallus, 20 weeks, male, SAMN16585374) | 34,698,652 | 37% | 28% |
SAMN16585375 | NA | Duodenum (Gallus gallus, 20 weeks, male, SAMN16585375) | 40,619,116 | 34% | 28% |
SAMN16585376 | NA | Duodenum (Gallus gallus, 20 weeks, female, SAMN16585376) | 63,564,738 | 38% | 33% |
SAMN16585377 | NA | Duodenum (Gallus gallus, 20 weeks, female, SAMN16585377) | 102,131,714 | 39% | 25% |
SAMN16585378 | NA | Esophagus (Gallus gallus, 20 weeks, male, SAMN16585378) | 77,095,956 | 41% | 14% |
SAMN16585379 | NA | Esophagus (Gallus gallus, 20 weeks, male, SAMN16585379) | 37,593,048 | 39% | 16% |
SAMN16585380 | NA | Esophagus (Gallus gallus, 20 weeks, female, SAMN16585380) | 38,109,036 | 37% | 30% |
SAMN16585381 | NA | Esophagus (Gallus gallus, 20 weeks, female, SAMN16585381) | 52,115,582 | 42% | 16% |
SAMN16585382 | NA | Gizzard (Gallus gallus, 20 weeks, male, SAMN16585382) | 16,757,788 | 36% | 40% |
SAMN16585383 | NA | Gizzard (Gallus gallus, 20 weeks, male, SAMN16585383) | 18,217,578 | 37% | 38% |
SAMN16585384 | NA | Gizzard (Gallus gallus, 20 weeks, female, SAMN16585384) | 53,548,268 | 38% | 33% |
SAMN16585385 | NA | Heart (Gallus gallus, 20 weeks, male, SAMN16585385) | 24,322,640 | 31% | 29% |
SAMN16585386 | NA | Heart (Gallus gallus, 20 weeks, male, SAMN16585386) | 49,273,650 | 35% | 30% |
SAMN16585387 | NA | Heart (Gallus gallus, 20 weeks, female, SAMN16585387) | 26,535,652 | 36% | 35% |
SAMN16585388 | NA | Heart (Gallus gallus, 20 weeks, female, SAMN16585388) | 60,240,362 | 35% | 35% |
SAMN16585389 | NA | Hypothalamus (Gallus gallus, 20 weeks, female, SAMN16585389) | 33,394,728 | 41% | 27% |
SAMN16585390 | NA | Hypothalamus (Gallus gallus, 20 weeks, female, SAMN16585390) | 46,376,888 | 39% | 29% |
SAMN16585391 | NA | Hypothalamus (Gallus gallus, 20 weeks, male, SAMN16585391) | 19,495,878 | 31% | 27% |
SAMN16585392 | NA | Hypothalamus (Gallus gallus, 20 weeks, male, SAMN16585392) | 21,740,930 | 35% | 30% |
SAMN16585393 | NA | Ileum (Gallus gallus, 20 weeks, male, SAMN16585393) | 25,887,390 | 39% | 28% |
SAMN16585394 | NA | Ileum (Gallus gallus, 20 weeks, male, SAMN16585394) | 25,224,666 | 38% | 32% |
SAMN16585395 | NA | Ileum (Gallus gallus, 20 weeks, female, SAMN16585395) | 59,968,480 | 39% | 38% |
SAMN16585396 | NA | Ileum (Gallus gallus, 20 weeks, female, SAMN16585396) | 61,442,554 | 38% | 36% |
SAMN16585397 | NA | Jejunum (Gallus gallus, 20 weeks, male, SAMN16585397) | 17,928,550 | 38% | 34% |
SAMN16585398 | NA | Jejunum (Gallus gallus, 20 weeks, male, SAMN16585398) | 23,263,806 | 35% | 26% |
SAMN16585399 | NA | Jejunum (Gallus gallus, 20 weeks, female, SAMN16585399) | 26,448,656 | 40% | 34% |
SAMN16585400 | NA | Jejunum (Gallus gallus, 20 weeks, female, SAMN16585400) | 35,446,302 | 39% | 39% |
SAMN16585401 | NA | Kidney (Gallus gallus, 20 weeks, male, SAMN16585401) | 24,156,570 | 40% | 41% |
SAMN16585402 | NA | Kidney (Gallus gallus, 20 weeks, male, SAMN16585402) | 19,008,634 | 42% | 29% |
SAMN16585403 | NA | Kidney (Gallus gallus, 20 weeks, female, SAMN16585403) | 72,730,590 | 39% | 51% |
SAMN16585404 | NA | Kidney (Gallus gallus, 20 weeks, female, SAMN16585404) | 42,822,380 | 42% | 41% |
SAMN16585405 | NA | Liver (Gallus gallus, 20 weeks, male, SAMN16585405) | 34,756,708 | 37% | 58% |
SAMN16585406 | NA | Liver (Gallus gallus, 20 weeks, female, SAMN16585406) | 29,691,748 | 39% | 40% |
SAMN16585407 | NA | Liver (Gallus gallus, 20 weeks, female, SAMN16585407) | 51,776,340 | 43% | 42% |
SAMN16585408 | NA | Liver (Gallus gallus, 20 weeks, male, SAMN16585408) | 21,355,456 | 41% | 50% |
SAMN16585409 | NA | Lung (Gallus gallus, 20 weeks, male, SAMN16585409) | 60,317,190 | 44% | 27% |
SAMN16585410 | NA | Lung (Gallus gallus, 20 weeks, male, SAMN16585410) | 29,533,382 | 43% | 27% |
SAMN16585411 | NA | Lung (Gallus gallus, 20 weeks, female, SAMN16585411) | 51,575,660 | 42% | 28% |
SAMN16585412 | NA | Lung (Gallus gallus, 20 weeks, female, SAMN16585412) | 42,261,360 | 40% | 26% |
SAMN16585413 | NA | Muscle (Gallus gallus, 20 weeks, female, SAMN16585413) | 40,545,678 | 38% | 38% |
SAMN16585414 | NA | Muscle (Gallus gallus, 20 weeks, female, SAMN16585414) | 31,871,648 | 36% | 33% |
SAMN16585415 | NA | Muscle (Gallus gallus, 20 weeks, male, SAMN16585415) | 34,883,006 | 37% | 37% |
SAMN16585416 | NA | Muscle (Gallus gallus, 20 weeks, male, SAMN16585416) | 37,371,258 | 38% | 42% |
SAMN16585417 | NA | Ovary (Gallus gallus, 20 weeks, female, SAMN16585417) | 85,695,582 | 37% | 36% |
SAMN16585418 | NA | Ovary (Gallus gallus, 20 weeks, female, SAMN16585418) | 65,562,992 | 39% | 27% |
SAMN16585419 | NA | Spleen (Gallus gallus, 20 weeks, male, SAMN16585419) | 52,708,494 | 41% | 34% |
SAMN16585420 | NA | Spleen (Gallus gallus, 20 weeks, female, SAMN16585420) | 36,746,136 | 43% | 32% |
SAMN16585421 | NA | Spleen (Gallus gallus, 20 weeks, female, SAMN16585421) | 43,966,666 | 38% | 24% |
SAMN16585422 | NA | Spleen (Gallus gallus, 20 weeks, male, SAMN16585422) | 40,936,772 | 39% | 28% |
SAMN16585423 | NA | Testis (Gallus gallus, 20 weeks, male, SAMN16585423) | 29,719,942 | 42% | 40% |
SAMN16585424 | NA | Testis (Gallus gallus, 20 weeks, male, SAMN16585424) | 34,177,708 | 36% | 35% |
SAMN16585425 | NA | Thymus (Gallus gallus, 20 weeks, male, SAMN16585425) | 111,246,204 | 43% | 36% |
SAMN16585426 | NA | Thymus (Gallus gallus, 20 weeks, male, SAMN16585426) | 30,111,064 | 40% | 29% |
SAMN16585427 | NA | Thymus (Gallus gallus, 20 weeks, female, SAMN16585427) | 15,670,588 | 39% | 20% |
SAMN16585428 | NA | Thymus (Gallus gallus, 20 weeks, female, SAMN16585428) | 72,338,028 | 39% | 32% |
SAMN16585429 | NA | Trachea (Gallus gallus, 20 weeks, male, SAMN16585429) | 60,241,030 | 44% | 17% |
SAMN16585430 | NA | Trachea (Gallus gallus, 20 weeks, male, SAMN16585430) | 42,704,146 | 44% | 14% |
SRA Long Read Alignment Statistics
The following long read RNA-Seq reads (PacBio, Oxford Nanopore, 454, or other long-read sequencing technologies) from the Sequence Read Archive were also used for gene prediction:
Run | Sample | Number of reads | Number (%) of sequences aligned by Minimap2 | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|---|
All | NA | 57522894 | 54567900 (94.86%) | 44782314 (77.85%) | 96.77 | 91.29 |
ERR2286007 | SAMEA104569410 | 148832 | 148417 (99.72%) | 124038 (83.34%) | 97.88 | 98.76 |
ERR2365562 | SAMEA104667332 | 152263 | 151917 (99.77%) | 127968 (84.04%) | 97.67 | 98.91 |
ERR2365563 | SAMEA104667333 | 210576 | 188165 (89.35%) | 114878 (54.55%) | 94.34 | 95.68 |
ERR2365565 | SAMEA104667338 | 153611 | 152671 (99.38%) | 109812 (71.48%) | 97.72 | 98.96 |
ERR2368565 | SAMEA104667777 | 422163 | 415062 (98.31%) | 326262 (77.28%) | 97.24 | 98.96 |
ERR7563950 | SAMEA9122905 | 1433290 | 1401920 (97.81%) | 1359214 (94.83%) | 99.64 | 99.82 |
ERR7563951 | SAMEA9122905 | 25280 | 24841 (98.26%) | 23317 (92.23%) | 99.52 | 99.55 |
ERR7563952 | SAMEA9122905 | 34893 | 34281 (98.24%) | 30577 (87.63%) | 99.38 | 98.37 |
ERR7563953 | SAMEA9122905 | 60173 | 59122 (98.25%) | 53894 (89.56%) | 99.44 | 98.88 |
ERR7563954 | SAMEA9122906 | 1044206 | 1039761 (99.57%) | 990218 (94.82%) | 99.64 | 99.83 |
ERR7563955 | SAMEA9122906 | 26377 | 26235 (99.46%) | 24817 (94.08%) | 99.56 | 99.75 |
ERR7563956 | SAMEA9122906 | 33613 | 33382 (99.31%) | 30882 (91.87%) | 99.43 | 99.43 |
ERR7563957 | SAMEA9122906 | 59990 | 59617 (99.37%) | 55699 (92.84%) | 99.49 | 99.57 |
ERR7563958 | SAMEA9122909 | 741535 | 731839 (98.69%) | 704496 (95.00%) | 99.62 | 99.86 |
ERR7563959 | SAMEA9122909 | 20350 | 20170 (99.11%) | 19097 (93.84%) | 99.58 | 99.79 |
ERR7563960 | SAMEA9122909 | 33091 | 32833 (99.22%) | 30043 (90.78%) | 99.43 | 99.49 |
ERR7563961 | SAMEA9122909 | 53441 | 53003 (99.18%) | 49139 (91.95%) | 99.49 | 99.61 |
ERR7563962 | SAMEA9122907 | 1458829 | 1450807 (99.45%) | 1383906 (94.86%) | 99.64 | 99.83 |
ERR7563963 | SAMEA9122907 | 34358 | 34160 (99.42%) | 32144 (93.55%) | 99.53 | 99.71 |
ERR7563964 | SAMEA9122907 | 35786 | 35543 (99.32%) | 32733 (91.46%) | 99.41 | 99.41 |
ERR7563965 | SAMEA9122907 | 70144 | 69703 (99.37%) | 64877 (92.49%) | 99.47 | 99.56 |
ERR7563966 | SAMEA9122908 | 1068939 | 1060445 (99.20%) | 1005358 (94.05%) | 99.63 | 99.82 |
ERR7563967 | SAMEA9122908 | 23837 | 23677 (99.32%) | 22351 (93.76%) | 99.56 | 99.78 |
ERR7563968 | SAMEA9122908 | 40274 | 40075 (99.50%) | 36843 (91.48%) | 99.42 | 99.35 |
ERR7563969 | SAMEA9122908 | 64111 | 63752 (99.44%) | 59194 (92.33%) | 99.47 | 99.51 |
ERR7563970 | SAMEA9122910 | 737715 | 732272 (99.26%) | 700428 (94.94%) | 99.61 | 99.74 |
ERR7563971 | SAMEA9122910 | 23504 | 23321 (99.22%) | 22243 (94.63%) | 99.49 | 99.49 |
ERR7563972 | SAMEA9122910 | 40412 | 40082 (99.18%) | 37159 (91.95%) | 99.28 | 98.44 |
ERR7563973 | SAMEA9122910 | 63916 | 63404 (99.19%) | 59402 (92.93%) | 99.36 | 98.83 |
ERR7563974 | SAMEA9122911 | 1056347 | 1049983 (99.39%) | 988782 (93.60%) | 99.61 | 99.82 |
ERR7563975 | SAMEA9122911 | 27418 | 27272 (99.46%) | 25694 (93.71%) | 99.54 | 99.75 |
ERR7563976 | SAMEA9122911 | 41115 | 40863 (99.38%) | 37649 (91.56%) | 99.4 | 99.36 |
ERR7563977 | SAMEA9122911 | 68533 | 68135 (99.41%) | 63343 (92.42%) | 99.46 | 99.52 |
ERR7563978 | SAMEA9122912 | 1155021 | 1138489 (98.56%) | 1101585 (95.37%) | 99.69 | 99.73 |
ERR7563979 | SAMEA9122912 | 18347 | 18040 (98.32%) | 16982 (92.56%) | 99.52 | 99.24 |
ERR7563980 | SAMEA9122912 | 37873 | 37360 (98.64%) | 33542 (88.56%) | 99.41 | 95.66 |
ERR7563981 | SAMEA9122912 | 56220 | 55400 (98.54%) | 50524 (89.86%) | 99.45 | 96.86 |
ERR7563982 | SAMEA9122913 | 1045365 | 1025483 (98.09%) | 984314 (94.15%) | 99.64 | 99.8 |
ERR7563983 | SAMEA9122913 | 26543 | 26167 (98.58%) | 24441 (92.08%) | 99.48 | 99.65 |
ERR7563984 | SAMEA9122913 | 44223 | 43691 (98.79%) | 38807 (87.75%) | 99.32 | 99.09 |
ERR7563985 | SAMEA9122913 | 70766 | 69858 (98.71%) | 63248 (89.37%) | 99.38 | 99.31 |
ERR7563986 | SAMEA9122916 | 924714 | 913662 (98.80%) | 890565 (96.30%) | 99.65 | 99.85 |
ERR7563987 | SAMEA9122916 | 17999 | 17752 (98.62%) | 16839 (93.55%) | 99.56 | 99.8 |
ERR7563988 | SAMEA9122916 | 33170 | 32903 (99.19%) | 29837 (89.95%) | 99.42 | 99.37 |
ERR7563989 | SAMEA9122916 | 51169 | 50655 (98.99%) | 46676 (91.21%) | 99.47 | 99.53 |
ERR7563990 | SAMEA9122914 | 776261 | 752043 (96.88%) | 723534 (93.20%) | 99.62 | 99.52 |
ERR7563991 | SAMEA9122914 | 26918 | 26538 (98.58%) | 25376 (94.27%) | 99.5 | 99.41 |
ERR7563992 | SAMEA9122914 | 54386 | 53722 (98.77%) | 48914 (89.93%) | 99.34 | 95.89 |
ERR7563993 | SAMEA9122914 | 81304 | 80260 (98.71%) | 74292 (91.37%) | 99.39 | 97.09 |
ERR7563994 | SAMEA9122915 | 653011 | 624164 (95.58%) | 582740 (89.23%) | 99.67 | 99.79 |
ERR7563995 | SAMEA9122915 | 12957 | 12547 (96.83%) | 11685 (90.18%) | 99.53 | 99.66 |
ERR7563996 | SAMEA9122915 | 23472 | 22959 (97.81%) | 20591 (87.72%) | 99.37 | 99.03 |
ERR7563997 | SAMEA9122915 | 36429 | 35506 (97.46%) | 32276 (88.59%) | 99.42 | 99.26 |
ERR7563998 | SAMEA9122916 | 720109 | 710683 (98.69%) | 694354 (96.42%) | 99.65 | 99.86 |
ERR7563999 | SAMEA9122916 | 14377 | 14174 (98.58%) | 13486 (93.80%) | 99.58 | 99.83 |
ERR7564000 | SAMEA9122916 | 27577 | 27342 (99.14%) | 24987 (90.60%) | 99.43 | 99.42 |
ERR7564001 | SAMEA9122916 | 41954 | 41516 (98.95%) | 38473 (91.70%) | 99.48 | 99.57 |
ERR7564002 | SAMEA9122914 | 438881 | 419057 (95.48%) | 405383 (92.36%) | 99.62 | 99.51 |
ERR7564003 | SAMEA9122914 | 16167 | 15842 (97.98%) | 15161 (93.77%) | 99.52 | 99.54 |
ERR7564004 | SAMEA9122914 | 35310 | 34843 (98.67%) | 31976 (90.55%) | 99.37 | 96.31 |
ERR7564005 | SAMEA9122914 | 51477 | 50685 (98.46%) | 47137 (91.56%) | 99.42 | 97.35 |
ERR7564006 | SAMEA9122915 | 325211 | 309280 (95.10%) | 288861 (88.82%) | 99.66 | 99.77 |
ERR7564007 | SAMEA9122915 | 8081 | 7811 (96.65%) | 7300 (90.33%) | 99.55 | 99.66 |
ERR7564008 | SAMEA9122915 | 14525 | 14159 (97.48%) | 12771 (87.92%) | 99.37 | 99.11 |
ERR7564009 | SAMEA9122915 | 22606 | 21970 (97.18%) | 20071 (88.78%) | 99.43 | 99.31 |
ERR7564010 | SAMEA9122917 | 614691 | 598283 (97.33%) | 570371 (92.78%) | 99.63 | 99.82 |
ERR7564011 | SAMEA9122917 | 19973 | 19651 (98.38%) | 18605 (93.15%) | 99.54 | 99.71 |
ERR7564012 | SAMEA9122917 | 36335 | 35920 (98.85%) | 32311 (88.92%) | 99.39 | 99.27 |
ERR7564013 | SAMEA9122917 | 56308 | 55571 (98.69%) | 50916 (90.42%) | 99.44 | 99.43 |
ERR7564014 | SAMEA9122918 | 454139 | 444599 (97.89%) | 431380 (94.98%) | 99.58 | 99.73 |
ERR7564015 | SAMEA9122918 | 10751 | 10528 (97.92%) | 9941 (92.46%) | 99.53 | 99.56 |
ERR7564016 | SAMEA9122918 | 18668 | 18448 (98.82%) | 16566 (88.74%) | 99.4 | 98.89 |
ERR7564017 | SAMEA9122918 | 29419 | 28976 (98.49%) | 26507 (90.10%) | 99.45 | 99.14 |
ERR7564018 | SAMEA9122919 | 464115 | 433678 (93.44%) | 419351 (90.35%) | 99.65 | 99.79 |
ERR7564019 | SAMEA9122919 | 8764 | 8348 (95.25%) | 7858 (89.66%) | 99.55 | 99.74 |
ERR7564020 | SAMEA9122919 | 15185 | 14628 (96.33%) | 12668 (83.42%) | 99.35 | 98.68 |
ERR7564021 | SAMEA9122919 | 23949 | 22976 (95.93%) | 20526 (85.70%) | 99.42 | 99.08 |
ERR7564022 | SAMEA9122920 | 345585 | 315194 (91.20%) | 304892 (88.22%) | 99.57 | 99.69 |
ERR7564023 | SAMEA9122920 | 11995 | 11533 (96.14%) | 10870 (90.62%) | 99.49 | 99.62 |
ERR7564024 | SAMEA9122920 | 23589 | 22839 (96.82%) | 20218 (85.70%) | 99.28 | 98.12 |
ERR7564025 | SAMEA9122920 | 35584 | 34373 (96.59%) | 31088 (87.36%) | 99.35 | 98.64 |
ERR7564026 | SAMEA9122917 | 636958 | 626208 (98.31%) | 594075 (93.26%) | 99.6 | 99.86 |
ERR7564027 | SAMEA9122917 | 21018 | 20774 (98.83%) | 19663 (93.55%) | 99.55 | 99.78 |
ERR7564028 | SAMEA9122917 | 37467 | 37176 (99.22%) | 33480 (89.35%) | 99.36 | 99.38 |
ERR7564029 | SAMEA9122917 | 58485 | 57950 (99.08%) | 53142 (90.86%) | 99.43 | 99.53 |
ERR7564030 | SAMEA9122918 | 1530168 | 1506952 (98.48%) | 1457398 (95.24%) | 99.6 | 99.77 |
ERR7564031 | SAMEA9122918 | 26016 | 25669 (98.66%) | 23991 (92.21%) | 99.51 | 99.54 |
ERR7564032 | SAMEA9122918 | 41136 | 40730 (99.01%) | 36053 (87.64%) | 99.37 | 98.56 |
ERR7564033 | SAMEA9122918 | 67152 | 66399 (98.87%) | 60044 (89.41%) | 99.42 | 98.95 |
ERR7564034 | SAMEA9122919 | 1831327 | 1738041 (94.90%) | 1669885 (91.18%) | 99.64 | 99.8 |
ERR7564035 | SAMEA9122919 | 21393 | 20565 (96.12%) | 18891 (88.30%) | 99.47 | 99.6 |
ERR7564036 | SAMEA9122919 | 36160 | 34995 (96.77%) | 29662 (82.02%) | 99.3 | 98.16 |
ERR7564037 | SAMEA9122919 | 57553 | 55560 (96.53%) | 48553 (84.36%) | 99.36 | 98.72 |
ERR7564038 | SAMEA9122920 | 1654668 | 1561945 (94.39%) | 1506599 (91.05%) | 99.57 | 99.72 |
ERR7564039 | SAMEA9122920 | 38197 | 37062 (97.02%) | 34368 (89.97%) | 99.43 | 99.43 |
ERR7564040 | SAMEA9122920 | 66033 | 64450 (97.60%) | 55911 (84.67%) | 99.25 | 97.58 |
ERR7564041 | SAMEA9122920 | 104230 | 101512 (97.39%) | 90280 (86.61%) | 99.32 | 98.28 |
ERR7564042 | SAMEA9122923 | 1665472 | 1567715 (94.13%) | 1508746 (90.58%) | 99.56 | 99.76 |
ERR7564043 | SAMEA9122923 | 31968 | 31105 (97.30%) | 29038 (90.83%) | 99.45 | 99.6 |
ERR7564044 | SAMEA9122923 | 50729 | 49799 (98.16%) | 44526 (87.77%) | 99.27 | 98.82 |
ERR7564045 | SAMEA9122923 | 82697 | 80903 (97.83%) | 73564 (88.95%) | 99.34 | 99.13 |
ERR7564046 | SAMEA9122921 | 1561594 | 1474762 (94.43%) | 1381291 (88.45%) | 99.55 | 99.65 |
ERR7564047 | SAMEA9122921 | 40705 | 39670 (97.45%) | 36657 (90.05%) | 99.36 | 99.3 |
ERR7564048 | SAMEA9122921 | 68993 | 67659 (98.06%) | 59333 (85.99%) | 99.2 | 97.58 |
ERR7564049 | SAMEA9122921 | 109698 | 107329 (97.84%) | 95990 (87.50%) | 99.26 | 98.24 |
ERR7564050 | SAMEA9122922 | 323199 | 300698 (93.03%) | 279766 (86.56%) | 99.66 | 99.83 |
ERR7564051 | SAMEA9122922 | 9272 | 8914 (96.13%) | 8441 (91.03%) | 99.56 | 99.78 |
ERR7564052 | SAMEA9122922 | 16728 | 16291 (97.38%) | 14769 (88.28%) | 99.37 | 99.18 |
ERR7564053 | SAMEA9122922 | 26000 | 25205 (96.94%) | 23210 (89.26%) | 99.44 | 99.4 |
ERR7564054 | SAMEA9122924 | 637060 | 581493 (91.27%) | 556151 (87.29%) | 99.56 | 99.72 |
ERR7564055 | SAMEA9122924 | 23498 | 22711 (96.65%) | 21369 (90.93%) | 99.5 | 99.65 |
ERR7564056 | SAMEA9122924 | 44090 | 43101 (97.75%) | 38385 (87.06%) | 99.32 | 98.64 |
ERR7564057 | SAMEA9122924 | 67588 | 65812 (97.37%) | 59754 (88.40%) | 99.38 | 99 |
ERR7564058 | SAMEA9122925 | 624471 | 601270 (96.28%) | 582691 (93.30%) | 99.63 | 99.77 |
ERR7564059 | SAMEA9122925 | 16398 | 16072 (98.01%) | 15236 (92.91%) | 99.53 | 99.67 |
ERR7564060 | SAMEA9122925 | 29983 | 29614 (98.76%) | 26842 (89.52%) | 99.38 | 98.61 |
ERR7564061 | SAMEA9122925 | 46381 | 45686 (98.50%) | 42078 (90.72%) | 99.43 | 98.99 |
ERR7564062 | SAMEA9122922 | 786377 | 730749 (92.92%) | 679937 (86.46%) | 99.66 | 99.84 |
ERR7564063 | SAMEA9122922 | 16865 | 16268 (96.46%) | 15333 (90.91%) | 99.53 | 99.73 |
ERR7564064 | SAMEA9122922 | 29248 | 28544 (97.59%) | 25570 (87.42%) | 99.36 | 99.02 |
ERR7564065 | SAMEA9122922 | 46113 | 44812 (97.17%) | 40903 (88.70%) | 99.43 | 99.29 |
ERR7564066 | SAMEA9122924 | 371375 | 340020 (91.55%) | 325213 (87.56%) | 99.56 | 99.73 |
ERR7564067 | SAMEA9122924 | 15967 | 15435 (96.66%) | 14663 (91.83%) | 99.52 | 99.7 |
ERR7564068 | SAMEA9122924 | 31170 | 30451 (97.69%) | 27489 (88.19%) | 99.34 | 98.8 |
ERR7564069 | SAMEA9122924 | 47137 | 45886 (97.34%) | 42153 (89.42%) | 99.4 | 99.12 |
ERR7564070 | SAMEA9122925 | 493893 | 478125 (96.80%) | 462494 (93.64%) | 99.63 | 99.8 |
ERR7564071 | SAMEA9122925 | 14550 | 14314 (98.37%) | 13612 (93.55%) | 99.56 | 99.75 |
ERR7564072 | SAMEA9122925 | 26929 | 26584 (98.71%) | 24111 (89.53%) | 99.4 | 98.8 |
ERR7564073 | SAMEA9122925 | 41479 | 40898 (98.59%) | 37722 (90.94%) | 99.46 | 99.15 |
SRR12888486 | SAMN16540004 | 602999 | 576590 (95.62%) | 367456 (60.93%) | 91.36 | 75.37 |
SRR12888487 | SAMN16540035 | 229171 | 211957 (92.48%) | 140044 (61.10%) | 91.26 | 72.29 |
SRR12888488 | SAMN16540034 | 242512 | 229643 (94.69%) | 145707 (60.08%) | 91.42 | 76.1 |
SRR12888489 | SAMN16540033 | 200928 | 187717 (93.42%) | 118866 (59.15%) | 91.37 | 75.43 |
SRR12888490 | SAMN16540032 | 378185 | 340661 (90.07%) | 218458 (57.76%) | 91.34 | 75.46 |
SRR12888491 | SAMN16540031 | 430919 | 391398 (90.82%) | 249509 (57.90%) | 91.32 | 72.32 |
SRR12888492 | SAMN16540030 | 1279 | 843 (65.91%) | 440 (34.40%) | 89.82 | 73.93 |
SRR12888493 | SAMN16540029 | 320225 | 294255 (91.89%) | 183862 (57.41%) | 91.33 | 75.4 |
SRR12888494 | SAMN16540028 | 369980 | 339744 (91.82%) | 224982 (60.80%) | 91.28 | 76.84 |
SRR12888495 | SAMN16540027 | 233377 | 194957 (83.53%) | 130265 (55.81%) | 91.23 | 73.04 |
SRR12888496 | SAMN16540026 | 405439 | 371483 (91.62%) | 247051 (60.93%) | 91.4 | 77.43 |
SRR12888497 | SAMN16540025 | 728371 | 655832 (90.04%) | 438103 (60.14%) | 91.37 | 76.68 |
SRR12888498 | SAMN16540024 | 347366 | 319911 (92.09%) | 207481 (59.72%) | 91.28 | 71.88 |
SRR12888499 | SAMN16540023 | 250445 | 231881 (92.58%) | 150251 (59.99%) | 91.32 | 72.81 |
SRR12888500 | SAMN16540022 | 247189 | 226598 (91.66%) | 143076 (57.88%) | 91.32 | 71.63 |
SRR12888501 | SAMN16540021 | 736071 | 692515 (94.08%) | 449169 (61.02%) | 91.4 | 75.35 |
SRR12888502 | SAMN16540020 | 390194 | 342048 (87.66%) | 225220 (57.72%) | 91.33 | 76.64 |
SRR12888503 | SAMN16540019 | 365152 | 318166 (87.13%) | 205609 (56.30%) | 91.29 | 72.57 |
SRR12888504 | SAMN16540018 | 378680 | 333220 (87.99%) | 222198 (58.67%) | 91.36 | 75.86 |
SRR12888505 | SAMN16540052 | 189889 | 169098 (89.05%) | 112463 (59.22%) | 91.36 | 76.05 |
SRR12888506 | SAMN16540051 | 279852 | 247793 (88.54%) | 156178 (55.80%) | 91.23 | 72.97 |
SRR12888507 | SAMN16540050 | 402570 | 356915 (88.65%) | 229504 (57.00%) | 91.17 | 72.76 |
SRR12888508 | SAMN16540049 | 235778 | 220869 (93.67%) | 139680 (59.24%) | 91.33 | 75.13 |
SRR12888509 | SAMN16539965 | 414871 | 382047 (92.08%) | 249722 (60.19%) | 91.31 | 71.86 |
SRR12888510 | SAMN16539964 | 353100 | 332037 (94.03%) | 217969 (61.73%) | 91.43 | 75.31 |
SRR12888511 | SAMN16539963 | 388768 | 365834 (94.10%) | 237955 (61.20%) | 91.41 | 75.12 |
SRR12888512 | SAMN16539962 | 489236 | 396060 (80.95%) | 255128 (52.14%) | 91.44 | 74.96 |
SRR12888513 | SAMN16539961 | 396521 | 348334 (87.84%) | 221232 (55.79%) | 91.46 | 75.69 |
SRR12888514 | SAMN16540000 | 271947 | 236569 (86.99%) | 157221 (57.81%) | 91.29 | 75.84 |
SRR12888515 | SAMN16539999 | 185299 | 148563 (80.17%) | 96864 (52.27%) | 91.26 | 72.64 |
SRR12888516 | SAMN16539998 | 315517 | 276291 (87.56%) | 183458 (58.14%) | 91.37 | 75.97 |
SRR12888517 | SAMN16539997 | 200797 | 180975 (90.12%) | 119419 (59.47%) | 91.32 | 76.32 |
SRR12888518 | SAMN16539996 | 309333 | 282381 (91.28%) | 182087 (58.86%) | 91.32 | 71.9 |
SRR12888519 | SAMN16539995 | 396758 | 366183 (92.29%) | 233689 (58.89%) | 91.39 | 72.35 |
SRR12888520 | SAMN16539994 | 498641 | 468513 (93.95%) | 299530 (60.06%) | 91.38 | 75.06 |
SRR12888521 | SAMN16539993 | 308848 | 292522 (94.71%) | 188964 (61.18%) | 91.39 | 76.09 |
SRR12888522 | SAMN16539992 | 239374 | 212280 (88.68%) | 135182 (56.47%) | 91.23 | 72.97 |
SRR12888523 | SAMN16539991 | 210815 | 187586 (88.98%) | 119426 (56.64%) | 91.32 | 73.8 |
SRR12888524 | SAMN16539990 | 332859 | 310944 (93.41%) | 197994 (59.48%) | 91.41 | 75.54 |
SRR12888525 | SAMN16539989 | 369632 | 337019 (91.17%) | 213525 (57.76%) | 91.29 | 75.24 |
SRR12888526 | SAMN16539988 | 294602 | 256048 (86.91%) | 168103 (57.06%) | 91.19 | 73.2 |
SRR12888527 | SAMN16539987 | 382839 | 333738 (87.17%) | 224877 (58.73%) | 91.18 | 73.46 |
SRR12888528 | SAMN16539986 | 414237 | 383768 (92.64%) | 258057 (62.29%) | 91.32 | 75.64 |
SRR12888529 | SAMN16539985 | 390435 | 363878 (93.19%) | 242966 (62.22%) | 91.29 | 75.67 |
SRR12888530 | SAMN16539984 | 325488 | 308869 (94.89%) | 195116 (59.94%) | 91.53 | 75.37 |
SRR12888531 | SAMN16539983 | 328931 | 293832 (89.32%) | 192973 (58.66%) | 91.32 | 72.43 |
SRR12888532 | SAMN16540017 | 314337 | 289434 (92.07%) | 183183 (58.27%) | 91.56 | 75.76 |
SRR12888533 | SAMN16540016 | 242368 | 224041 (92.43%) | 143222 (59.09%) | 91.55 | 75.88 |
SRR12888534 | SAMN16540015 | 420784 | 406583 (96.62%) | 277337 (65.90%) | 91.31 | 75.81 |
SRR12888535 | SAMN16540014 | 227341 | 212773 (93.59%) | 143560 (63.14%) | 91.21 | 73.43 |
SRR12888536 | SAMN16540013 | 296678 | 279516 (94.21%) | 186164 (62.74%) | 91.29 | 74.56 |
SRR12888537 | SAMN16540012 | 275008 | 262377 (95.40%) | 174721 (63.53%) | 91.25 | 75.37 |
SRR12888538 | SAMN16540011 | 322798 | 297709 (92.22%) | 177203 (54.89%) | 91.43 | 76.18 |
SRR12888539 | SAMN16539937 | 203102 | 181443 (89.33%) | 114893 (56.56%) | 91.36 | 73.24 |
SRR12888540 | SAMN16539936 | 264583 | 250588 (94.71%) | 148153 (55.99%) | 91.57 | 75.99 |
SRR12888541 | SAMN16539935 | 573338 | 542928 (94.69%) | 330064 (57.56%) | 91.4 | 75.45 |
SRR12888542 | SAMN16539934 | 550308 | 516124 (93.78%) | 323125 (58.71%) | 91.31 | 71.68 |
SRR12888543 | SAMN16539933 | 405381 | 379439 (93.60%) | 240356 (59.29%) | 91.26 | 72.79 |
SRR12888544 | SAMN16539932 | 826809 | 789374 (95.47%) | 505615 (61.15%) | 91.3 | 75.58 |
SRR12888545 | SAMN16539931 | 127318 | 117955 (92.64%) | 74130 (58.22%) | 91.3 | 72.51 |
SRR12888546 | SAMN16539930 | 388572 | 371063 (95.49%) | 241189 (62.07%) | 91.33 | 75.26 |
SRR12888547 | SAMN16539929 | 442756 | 423689 (95.69%) | 277047 (62.57%) | 91.41 | 75.16 |
SRR12888548 | SAMN16539928 | 563236 | 530879 (94.25%) | 339488 (60.27%) | 91.36 | 74.98 |
SRR12888549 | SAMN16539960 | 196027 | 185761 (94.76%) | 122214 (62.34%) | 91.45 | 75.25 |
SRR12888550 | SAMN16539959 | 327373 | 306499 (93.62%) | 195781 (59.80%) | 91.35 | 72.36 |
SRR12888551 | SAMN16539958 | 304931 | 284742 (93.37%) | 179170 (58.75%) | 91.22 | 71.97 |
SRR12888552 | SAMN16539957 | 513055 | 489694 (95.44%) | 313046 (61.01%) | 91.36 | 75.24 |
SRR12888553 | SAMN16539956 | 215282 | 206388 (95.86%) | 137526 (63.88%) | 91.45 | 75.68 |
SRR13267647 | SAMN09930639 | 24248 | 23943 (98.74%) | 18328 (75.58%) | 98.72 | 99.57 |
SRR13267648 | SAMN09930637 | 31923 | 31773 (99.53%) | 25808 (80.84%) | 99.01 | 99.3 |
SRR13267649 | SAMN09930639 | 305309 | 300357 (98.37%) | 223244 (73.12%) | 98.17 | 98.35 |
SRR13267650 | SAMN09930638 | 44885 | 42250 (94.12%) | 37638 (83.85%) | 99.23 | 99.62 |
SRR13267651 | SAMN09930637 | 33584 | 31776 (94.61%) | 28021 (83.43%) | 99.21 | 99.68 |
SRR13267652 | SAMN09930638 | 27220 | 27147 (99.73%) | 20478 (75.23%) | 98.85 | 99.17 |
SRR13267653 | SAMN09930638 | 31137 | 30812 (98.95%) | 25736 (82.65%) | 99.09 | 99.62 |
SRR13267654 | SAMN09930637 | 272921 | 268784 (98.48%) | 202066 (74.03%) | 98.44 | 98.58 |
SRR13267655 | SAMN09930638 | 261160 | 256699 (98.29%) | 179554 (68.75%) | 98.02 | 98.22 |
SRR13267656 | SAMN09930639 | 29831 | 29665 (99.44%) | 23509 (78.80%) | 98.89 | 99.36 |
SRR13267657 | SAMN09930640 | 31581 | 29733 (94.14%) | 25623 (81.13%) | 99.03 | 99.63 |
SRR13267658 | SAMN09930640 | 27695 | 27618 (99.72%) | 21860 (78.93%) | 98.84 | 99.24 |
SRR13267659 | SAMN09930640 | 323571 | 318029 (98.28%) | 239662 (74.06%) | 98.09 | 98.29 |
SRR13267660 | SAMN09930640 | 26604 | 26351 (99.04%) | 21126 (79.40%) | 98.86 | 99.58 |
SRR13267661 | SAMN09930637 | 30806 | 30676 (99.57%) | 23444 (76.10%) | 98.93 | 99.34 |
SRR13267662 | SAMN09930639 | 67632 | 64204 (94.93%) | 55716 (82.38%) | 99.09 | 99.58 |
Run | Sample | Number of reads | Number (%) of sequences aligned by Minimap2 | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|---|
All | NA | 57522894 | 54953770 (95.53%) | 44896822 (78.05%) | 96.78 | 91.27 |
ERR2286007 | SAMEA104569410 | 148832 | 148451 (99.74%) | 124242 (83.47%) | 97.95 | 98.78 |
ERR2365562 | SAMEA104667332 | 152263 | 151901 (99.76%) | 128006 (84.06%) | 97.73 | 98.92 |
ERR2365563 | SAMEA104667333 | 210576 | 188453 (89.49%) | 114793 (54.51%) | 94.39 | 95.69 |
ERR2365565 | SAMEA104667338 | 153611 | 152761 (99.44%) | 109841 (71.50%) | 97.69 | 98.95 |
ERR2368565 | SAMEA104667777 | 422163 | 415510 (98.42%) | 325921 (77.20%) | 97.26 | 98.92 |
ERR7563950 | SAMEA9122905 | 1433290 | 1416374 (98.81%) | 1362051 (95.02%) | 99.63 | 99.8 |
ERR7563951 | SAMEA9122905 | 25280 | 24980 (98.81%) | 23319 (92.24%) | 99.49 | 99.51 |
ERR7563952 | SAMEA9122905 | 34893 | 34449 (98.72%) | 30664 (87.88%) | 99.34 | 98.16 |
ERR7563953 | SAMEA9122905 | 60173 | 59429 (98.76%) | 53983 (89.71%) | 99.4 | 98.74 |
ERR7563954 | SAMEA9122906 | 1044206 | 1039837 (99.58%) | 994671 (95.25%) | 99.61 | 99.83 |
ERR7563955 | SAMEA9122906 | 26377 | 26239 (99.47%) | 24764 (93.88%) | 99.52 | 99.73 |
ERR7563956 | SAMEA9122906 | 33613 | 33389 (99.33%) | 30816 (91.67%) | 99.39 | 99.42 |
ERR7563957 | SAMEA9122906 | 59990 | 59628 (99.39%) | 55580 (92.64%) | 99.45 | 99.56 |
ERR7563958 | SAMEA9122909 | 741535 | 735751 (99.21%) | 706446 (95.26%) | 99.6 | 99.85 |
ERR7563959 | SAMEA9122909 | 20350 | 20204 (99.28%) | 19058 (93.65%) | 99.55 | 99.79 |
ERR7563960 | SAMEA9122909 | 33091 | 32882 (99.36%) | 29992 (90.63%) | 99.4 | 99.45 |
ERR7563961 | SAMEA9122909 | 53441 | 53086 (99.33%) | 49050 (91.78%) | 99.46 | 99.58 |
ERR7563962 | SAMEA9122907 | 1458829 | 1450737 (99.44%) | 1388822 (95.20%) | 99.62 | 99.83 |
ERR7563963 | SAMEA9122907 | 34358 | 34178 (99.47%) | 32063 (93.32%) | 99.5 | 99.68 |
ERR7563964 | SAMEA9122907 | 35786 | 35541 (99.31%) | 32642 (91.21%) | 99.38 | 99.38 |
ERR7563965 | SAMEA9122907 | 70144 | 69719 (99.39%) | 64705 (92.24%) | 99.44 | 99.53 |
ERR7563966 | SAMEA9122908 | 1068939 | 1063667 (99.50%) | 1011080 (94.58%) | 99.6 | 99.82 |
ERR7563967 | SAMEA9122908 | 23837 | 23710 (99.46%) | 22317 (93.62%) | 99.52 | 99.77 |
ERR7563968 | SAMEA9122908 | 40274 | 40087 (99.53%) | 36735 (91.21%) | 99.39 | 99.36 |
ERR7563969 | SAMEA9122908 | 64111 | 63797 (99.51%) | 59052 (92.10%) | 99.44 | 99.52 |
ERR7563970 | SAMEA9122910 | 737715 | 733825 (99.47%) | 704109 (95.44%) | 99.58 | 99.72 |
ERR7563971 | SAMEA9122910 | 23504 | 23369 (99.42%) | 22215 (94.51%) | 99.45 | 99.45 |
ERR7563972 | SAMEA9122910 | 40412 | 40170 (99.40%) | 37137 (91.89%) | 99.25 | 98.39 |
ERR7563973 | SAMEA9122910 | 63916 | 63539 (99.41%) | 59352 (92.85%) | 99.32 | 98.79 |
ERR7563974 | SAMEA9122911 | 1056347 | 1054664 (99.84%) | 996029 (94.28%) | 99.57 | 99.81 |
ERR7563975 | SAMEA9122911 | 27418 | 27314 (99.62%) | 25666 (93.61%) | 99.5 | 99.74 |
ERR7563976 | SAMEA9122911 | 41115 | 40909 (99.49%) | 37589 (91.42%) | 99.36 | 99.34 |
ERR7563977 | SAMEA9122911 | 68533 | 68223 (99.54%) | 63255 (92.29%) | 99.42 | 99.5 |
ERR7563978 | SAMEA9122912 | 1155021 | 1145046 (99.13%) | 1104360 (95.61%) | 99.65 | 99.71 |
ERR7563979 | SAMEA9122912 | 18347 | 18169 (99.02%) | 16996 (92.63%) | 99.47 | 99.22 |
ERR7563980 | SAMEA9122912 | 37873 | 37541 (99.12%) | 33686 (88.94%) | 99.36 | 95.38 |
ERR7563981 | SAMEA9122912 | 56220 | 55710 (99.09%) | 50682 (90.14%) | 99.4 | 96.67 |
ERR7563982 | SAMEA9122913 | 1045365 | 1029346 (98.46%) | 986625 (94.38%) | 99.6 | 99.79 |
ERR7563983 | SAMEA9122913 | 26543 | 26193 (98.68%) | 24328 (91.65%) | 99.44 | 99.66 |
ERR7563984 | SAMEA9122913 | 44223 | 43718 (98.85%) | 38650 (87.39%) | 99.29 | 99.08 |
ERR7563985 | SAMEA9122913 | 70766 | 69911 (98.79%) | 62978 (88.99%) | 99.35 | 99.3 |
ERR7563986 | SAMEA9122916 | 924714 | 915458 (98.99%) | 891221 (96.37%) | 99.64 | 99.85 |
ERR7563987 | SAMEA9122916 | 17999 | 17793 (98.85%) | 16801 (93.34%) | 99.51 | 99.78 |
ERR7563988 | SAMEA9122916 | 33170 | 32919 (99.24%) | 29812 (89.87%) | 99.38 | 99.33 |
ERR7563989 | SAMEA9122916 | 51169 | 50712 (99.10%) | 46613 (91.09%) | 99.43 | 99.49 |
ERR7563990 | SAMEA9122914 | 776261 | 756360 (97.43%) | 726406 (93.57%) | 99.59 | 99.48 |
ERR7563991 | SAMEA9122914 | 26918 | 26586 (98.76%) | 25322 (94.07%) | 99.46 | 99.34 |
ERR7563992 | SAMEA9122914 | 54386 | 53799 (98.92%) | 49038 (90.16%) | 99.29 | 95.62 |
ERR7563993 | SAMEA9122914 | 81304 | 80385 (98.86%) | 74359 (91.45%) | 99.35 | 96.89 |
ERR7563994 | SAMEA9122915 | 653011 | 633179 (96.96%) | 581481 (89.04%) | 99.66 | 99.78 |
ERR7563995 | SAMEA9122915 | 12957 | 12587 (97.14%) | 11614 (89.63%) | 99.5 | 99.65 |
ERR7563996 | SAMEA9122915 | 23472 | 22972 (97.86%) | 20531 (87.47%) | 99.33 | 98.98 |
ERR7563997 | SAMEA9122915 | 36429 | 35559 (97.61%) | 32145 (88.24%) | 99.39 | 99.22 |
ERR7563998 | SAMEA9122916 | 720109 | 712130 (98.89%) | 694653 (96.46%) | 99.64 | 99.85 |
ERR7563999 | SAMEA9122916 | 14377 | 14199 (98.76%) | 13461 (93.62%) | 99.54 | 99.79 |
ERR7564000 | SAMEA9122916 | 27577 | 27339 (99.13%) | 24918 (90.35%) | 99.39 | 99.4 |
ERR7564001 | SAMEA9122916 | 41954 | 41538 (99.00%) | 38379 (91.47%) | 99.44 | 99.53 |
ERR7564002 | SAMEA9122914 | 438881 | 422093 (96.17%) | 406559 (92.63%) | 99.6 | 99.46 |
ERR7564003 | SAMEA9122914 | 16167 | 15874 (98.18%) | 15108 (93.44%) | 99.48 | 99.5 |
ERR7564004 | SAMEA9122914 | 35310 | 34872 (98.75%) | 31985 (90.58%) | 99.33 | 96.08 |
ERR7564005 | SAMEA9122914 | 51477 | 50746 (98.57%) | 47093 (91.48%) | 99.38 | 97.18 |
ERR7564006 | SAMEA9122915 | 325211 | 313665 (96.44%) | 288285 (88.64%) | 99.64 | 99.76 |
ERR7564007 | SAMEA9122915 | 8081 | 7830 (96.89%) | 7259 (89.82%) | 99.52 | 99.65 |
ERR7564008 | SAMEA9122915 | 14525 | 14171 (97.56%) | 12757 (87.82%) | 99.34 | 99.06 |
ERR7564009 | SAMEA9122915 | 22606 | 22001 (97.32%) | 20016 (88.54%) | 99.4 | 99.27 |
ERR7564010 | SAMEA9122917 | 614691 | 604600 (98.35%) | 572028 (93.05%) | 99.61 | 99.78 |
ERR7564011 | SAMEA9122917 | 19973 | 19724 (98.75%) | 18571 (92.98%) | 99.51 | 99.69 |
ERR7564012 | SAMEA9122917 | 36335 | 35950 (98.94%) | 32284 (88.85%) | 99.34 | 99.26 |
ERR7564013 | SAMEA9122917 | 56308 | 55674 (98.87%) | 50855 (90.31%) | 99.4 | 99.41 |
ERR7564014 | SAMEA9122918 | 454139 | 445054 (97.99%) | 431292 (94.96%) | 99.63 | 99.79 |
ERR7564015 | SAMEA9122918 | 10751 | 10438 (97.08%) | 9854 (91.65%) | 99.5 | 99.57 |
ERR7564016 | SAMEA9122918 | 18668 | 18381 (98.46%) | 16498 (88.37%) | 99.37 | 98.92 |
ERR7564017 | SAMEA9122918 | 29419 | 28819 (97.96%) | 26352 (89.57%) | 99.42 | 99.16 |
ERR7564018 | SAMEA9122919 | 464115 | 442908 (95.43%) | 420069 (90.50%) | 99.6 | 99.68 |
ERR7564019 | SAMEA9122919 | 8764 | 8405 (95.90%) | 7837 (89.42%) | 99.51 | 99.64 |
ERR7564020 | SAMEA9122919 | 15185 | 14708 (96.85%) | 12661 (83.37%) | 99.29 | 98.55 |
ERR7564021 | SAMEA9122919 | 23949 | 23113 (96.50%) | 20498 (85.59%) | 99.37 | 98.97 |
ERR7564022 | SAMEA9122920 | 345585 | 322980 (93.45%) | 305540 (88.41%) | 99.49 | 99.44 |
ERR7564023 | SAMEA9122920 | 11995 | 11590 (96.62%) | 10818 (90.18%) | 99.44 | 99.54 |
ERR7564024 | SAMEA9122920 | 23589 | 22921 (97.16%) | 20185 (85.56%) | 99.24 | 97.93 |
ERR7564025 | SAMEA9122920 | 35584 | 34511 (96.98%) | 31003 (87.12%) | 99.31 | 98.5 |
ERR7564026 | SAMEA9122917 | 636958 | 631825 (99.19%) | 596037 (93.57%) | 99.58 | 99.83 |
ERR7564027 | SAMEA9122917 | 21018 | 20838 (99.14%) | 19634 (93.41%) | 99.52 | 99.75 |
ERR7564028 | SAMEA9122917 | 37467 | 37212 (99.31%) | 33379 (89.08%) | 99.32 | 99.34 |
ERR7564029 | SAMEA9122917 | 58485 | 58050 (99.25%) | 53013 (90.64%) | 99.4 | 99.49 |
ERR7564030 | SAMEA9122918 | 1530168 | 1512396 (98.83%) | 1461721 (95.52%) | 99.62 | 99.81 |
ERR7564031 | SAMEA9122918 | 26016 | 25618 (98.47%) | 23891 (91.83%) | 99.48 | 99.53 |
ERR7564032 | SAMEA9122918 | 41136 | 40649 (98.81%) | 35897 (87.26%) | 99.34 | 98.58 |
ERR7564033 | SAMEA9122918 | 67152 | 66268 (98.68%) | 59788 (89.03%) | 99.4 | 98.96 |
ERR7564034 | SAMEA9122919 | 1831327 | 1775311 (96.94%) | 1670462 (91.21%) | 99.6 | 99.74 |
ERR7564035 | SAMEA9122919 | 21393 | 20694 (96.73%) | 18861 (88.16%) | 99.43 | 99.55 |
ERR7564036 | SAMEA9122919 | 36160 | 35179 (97.28%) | 29574 (81.78%) | 99.26 | 98.04 |
ERR7564037 | SAMEA9122919 | 57553 | 55874 (97.08%) | 48435 (84.15%) | 99.33 | 98.63 |
ERR7564038 | SAMEA9122920 | 1654668 | 1594686 (96.37%) | 1508103 (91.14%) | 99.5 | 99.56 |
ERR7564039 | SAMEA9122920 | 38197 | 37280 (97.59%) | 34204 (89.54%) | 99.38 | 99.36 |
ERR7564040 | SAMEA9122920 | 66033 | 64666 (97.92%) | 55862 (84.59%) | 99.21 | 97.34 |
ERR7564041 | SAMEA9122920 | 104230 | 101946 (97.80%) | 90066 (86.41%) | 99.27 | 98.11 |
ERR7564042 | SAMEA9122923 | 1665472 | 1607443 (96.51%) | 1511205 (90.73%) | 99.52 | 99.69 |
ERR7564043 | SAMEA9122923 | 31968 | 31312 (97.94%) | 28946 (90.54%) | 99.41 | 99.56 |
ERR7564044 | SAMEA9122923 | 50729 | 49918 (98.40%) | 44421 (87.56%) | 99.23 | 98.77 |
ERR7564045 | SAMEA9122923 | 82697 | 81230 (98.22%) | 73368 (88.71%) | 99.3 | 99.08 |
ERR7564046 | SAMEA9122921 | 1561594 | 1495635 (95.77%) | 1387127 (88.82%) | 99.52 | 99.56 |
ERR7564047 | SAMEA9122921 | 40705 | 39818 (97.82%) | 36569 (89.83%) | 99.33 | 99.27 |
ERR7564048 | SAMEA9122921 | 68993 | 67829 (98.31%) | 59371 (86.05%) | 99.16 | 97.34 |
ERR7564049 | SAMEA9122921 | 109698 | 107646 (98.12%) | 95940 (87.45%) | 99.23 | 98.08 |
ERR7564050 | SAMEA9122922 | 323199 | 307845 (95.24%) | 280091 (86.66%) | 99.63 | 99.73 |
ERR7564051 | SAMEA9122922 | 9272 | 8994 (97.00%) | 8434 (90.96%) | 99.51 | 99.66 |
ERR7564052 | SAMEA9122922 | 16728 | 16347 (97.72%) | 14715 (87.96%) | 99.33 | 99.11 |
ERR7564053 | SAMEA9122922 | 26000 | 25341 (97.46%) | 23149 (89.03%) | 99.4 | 99.31 |
ERR7564054 | SAMEA9122924 | 637060 | 595809 (93.52%) | 557784 (87.55%) | 99.51 | 99.55 |
ERR7564055 | SAMEA9122924 | 23498 | 22862 (97.29%) | 21344 (90.83%) | 99.45 | 99.59 |
ERR7564056 | SAMEA9122924 | 44090 | 43218 (98.02%) | 38384 (87.05%) | 99.28 | 98.49 |
ERR7564057 | SAMEA9122924 | 67588 | 66080 (97.76%) | 59729 (88.37%) | 99.34 | 98.88 |
ERR7564058 | SAMEA9122925 | 624471 | 608845 (97.49%) | 581875 (93.17%) | 99.57 | 99.69 |
ERR7564059 | SAMEA9122925 | 16398 | 16094 (98.14%) | 15188 (92.62%) | 99.5 | 99.62 |
ERR7564060 | SAMEA9122925 | 29983 | 29585 (98.67%) | 26787 (89.34%) | 99.35 | 98.56 |
ERR7564061 | SAMEA9122925 | 46381 | 45680 (98.48%) | 41975 (90.50%) | 99.4 | 98.95 |
ERR7564062 | SAMEA9122922 | 786377 | 749070 (95.25%) | 681055 (86.60%) | 99.64 | 99.73 |
ERR7564063 | SAMEA9122922 | 16865 | 16393 (97.20%) | 15311 (90.78%) | 99.49 | 99.64 |
ERR7564064 | SAMEA9122922 | 29248 | 28662 (97.99%) | 25511 (87.22%) | 99.33 | 98.94 |
ERR7564065 | SAMEA9122922 | 46113 | 45055 (97.70%) | 40822 (88.52%) | 99.39 | 99.2 |
ERR7564066 | SAMEA9122924 | 371375 | 347815 (93.65%) | 325986 (87.77%) | 99.52 | 99.57 |
ERR7564067 | SAMEA9122924 | 15967 | 15520 (97.20%) | 14637 (91.67%) | 99.48 | 99.65 |
ERR7564068 | SAMEA9122924 | 31170 | 30538 (97.97%) | 27471 (88.13%) | 99.3 | 98.64 |
ERR7564069 | SAMEA9122924 | 47137 | 46058 (97.71%) | 42108 (89.33%) | 99.36 | 98.99 |
ERR7564070 | SAMEA9122925 | 493893 | 483248 (97.84%) | 461917 (93.52%) | 99.57 | 99.72 |
ERR7564071 | SAMEA9122925 | 14550 | 14326 (98.46%) | 13552 (93.14%) | 99.52 | 99.71 |
ERR7564072 | SAMEA9122925 | 26929 | 26593 (98.75%) | 24033 (89.24%) | 99.36 | 98.69 |
ERR7564073 | SAMEA9122925 | 41479 | 40919 (98.64%) | 37585 (90.61%) | 99.42 | 99.06 |
SRR12888486 | SAMN16540004 | 602999 | 577776 (95.81%) | 370489 (61.44%) | 91.4 | 75.35 |
SRR12888487 | SAMN16540035 | 229171 | 212387 (92.67%) | 140858 (61.46%) | 91.29 | 72.26 |
SRR12888488 | SAMN16540034 | 242512 | 230149 (94.90%) | 146391 (60.36%) | 91.46 | 76.09 |
SRR12888489 | SAMN16540033 | 200928 | 188274 (93.70%) | 119461 (59.45%) | 91.42 | 75.39 |
SRR12888490 | SAMN16540032 | 378185 | 342216 (90.48%) | 219251 (57.97%) | 91.4 | 75.43 |
SRR12888491 | SAMN16540031 | 430919 | 392148 (91.00%) | 250304 (58.08%) | 91.36 | 72.26 |
SRR12888492 | SAMN16540030 | 1279 | 844 (65.98%) | 444 (34.71%) | 89.82 | 73.95 |
SRR12888493 | SAMN16540029 | 320225 | 295588 (92.30%) | 184775 (57.70%) | 91.38 | 75.38 |
SRR12888494 | SAMN16540028 | 369980 | 341007 (92.16%) | 226075 (61.10%) | 91.34 | 76.83 |
SRR12888495 | SAMN16540027 | 233377 | 196030 (83.99%) | 130661 (55.98%) | 91.28 | 73.02 |
SRR12888496 | SAMN16540026 | 405439 | 373162 (92.03%) | 248034 (61.17%) | 91.45 | 77.43 |
SRR12888497 | SAMN16540025 | 728371 | 659928 (90.60%) | 439816 (60.38%) | 91.42 | 76.66 |
SRR12888498 | SAMN16540024 | 347366 | 320516 (92.27%) | 207998 (59.87%) | 91.33 | 71.85 |
SRR12888499 | SAMN16540023 | 250445 | 232049 (92.65%) | 150755 (60.19%) | 91.37 | 72.76 |
SRR12888500 | SAMN16540022 | 247189 | 227040 (91.84%) | 143517 (58.05%) | 91.37 | 71.61 |
SRR12888501 | SAMN16540021 | 736071 | 694524 (94.35%) | 451368 (61.32%) | 91.45 | 75.32 |
SRR12888502 | SAMN16540020 | 390194 | 344182 (88.20%) | 226069 (57.93%) | 91.38 | 76.64 |
SRR12888503 | SAMN16540019 | 365152 | 318999 (87.36%) | 206118 (56.44%) | 91.34 | 72.56 |
SRR12888504 | SAMN16540018 | 378680 | 335359 (88.55%) | 222929 (58.87%) | 91.41 | 75.87 |
SRR12888505 | SAMN16540052 | 189889 | 169812 (89.42%) | 112859 (59.43%) | 91.4 | 76.06 |
SRR12888506 | SAMN16540051 | 279852 | 249307 (89.08%) | 156683 (55.98%) | 91.27 | 72.87 |
SRR12888507 | SAMN16540050 | 402570 | 358724 (89.10%) | 230169 (57.17%) | 91.21 | 72.7 |
SRR12888508 | SAMN16540049 | 235778 | 220910 (93.69%) | 139859 (59.31%) | 91.37 | 75.11 |
SRR12888509 | SAMN16539965 | 414871 | 383172 (92.35%) | 250324 (60.33%) | 91.36 | 71.83 |
SRR12888510 | SAMN16539964 | 353100 | 333379 (94.41%) | 218826 (61.97%) | 91.49 | 75.27 |
SRR12888511 | SAMN16539963 | 388768 | 366937 (94.38%) | 238948 (61.46%) | 91.46 | 75.12 |
SRR12888512 | SAMN16539962 | 489236 | 400674 (81.89%) | 255943 (52.31%) | 91.5 | 74.94 |
SRR12888513 | SAMN16539961 | 396521 | 350415 (88.37%) | 222074 (56.00%) | 91.52 | 75.66 |
SRR12888514 | SAMN16540000 | 271947 | 238177 (87.58%) | 157812 (58.03%) | 91.34 | 75.84 |
SRR12888515 | SAMN16539999 | 185299 | 149532 (80.69%) | 97169 (52.43%) | 91.3 | 72.55 |
SRR12888516 | SAMN16539998 | 315517 | 278193 (88.17%) | 184121 (58.35%) | 91.43 | 75.94 |
SRR12888517 | SAMN16539997 | 200797 | 181650 (90.46%) | 119864 (59.69%) | 91.37 | 76.34 |
SRR12888518 | SAMN16539996 | 309333 | 282966 (91.47%) | 182625 (59.03%) | 91.36 | 71.87 |
SRR12888519 | SAMN16539995 | 396758 | 366935 (92.48%) | 234294 (59.05%) | 91.42 | 72.32 |
SRR12888520 | SAMN16539994 | 498641 | 470401 (94.33%) | 300948 (60.35%) | 91.42 | 75.02 |
SRR12888521 | SAMN16539993 | 308848 | 293453 (95.01%) | 189792 (61.45%) | 91.44 | 76.1 |
SRR12888522 | SAMN16539992 | 239374 | 213101 (89.02%) | 135525 (56.61%) | 91.27 | 72.84 |
SRR12888523 | SAMN16539991 | 210815 | 188664 (89.49%) | 119778 (56.81%) | 91.36 | 73.64 |
SRR12888524 | SAMN16539990 | 332859 | 312263 (93.81%) | 198703 (59.69%) | 91.44 | 75.52 |
SRR12888525 | SAMN16539989 | 369632 | 338550 (91.59%) | 214296 (57.97%) | 91.33 | 75.26 |
SRR12888526 | SAMN16539988 | 294602 | 258281 (87.67%) | 168929 (57.34%) | 91.24 | 73.16 |
SRR12888527 | SAMN16539987 | 382839 | 336808 (87.97%) | 225880 (59.00%) | 91.23 | 73.43 |
SRR12888528 | SAMN16539986 | 414237 | 386446 (93.29%) | 259269 (62.58%) | 91.37 | 75.61 |
SRR12888529 | SAMN16539985 | 390435 | 365717 (93.66%) | 244129 (62.52%) | 91.34 | 75.66 |
SRR12888530 | SAMN16539984 | 325488 | 310234 (95.31%) | 196227 (60.28%) | 91.57 | 75.36 |
SRR12888531 | SAMN16539983 | 328931 | 295657 (89.88%) | 194320 (59.07%) | 91.35 | 72.34 |
SRR12888532 | SAMN16540017 | 314337 | 291226 (92.64%) | 184268 (58.62%) | 91.61 | 75.76 |
SRR12888533 | SAMN16540016 | 242368 | 225508 (93.04%) | 144215 (59.50%) | 91.59 | 75.87 |
SRR12888534 | SAMN16540015 | 420784 | 406543 (96.61%) | 277918 (66.04%) | 91.37 | 75.87 |
SRR12888535 | SAMN16540014 | 227341 | 212990 (93.68%) | 143905 (63.29%) | 91.26 | 73.42 |
SRR12888536 | SAMN16540013 | 296678 | 279214 (94.11%) | 186490 (62.85%) | 91.35 | 74.54 |
SRR12888537 | SAMN16540012 | 275008 | 261836 (95.21%) | 175054 (63.65%) | 91.31 | 75.44 |
SRR12888538 | SAMN16540011 | 322798 | 299976 (92.92%) | 178363 (55.25%) | 91.5 | 76.06 |
SRR12888539 | SAMN16539937 | 203102 | 181996 (89.60%) | 115267 (56.75%) | 91.44 | 73.17 |
SRR12888540 | SAMN16539936 | 264583 | 251876 (95.19%) | 148852 (56.25%) | 91.63 | 75.89 |
SRR12888541 | SAMN16539935 | 573338 | 545910 (95.21%) | 331931 (57.89%) | 91.46 | 75.4 |
SRR12888542 | SAMN16539934 | 550308 | 516259 (93.81%) | 323874 (58.85%) | 91.37 | 71.67 |
SRR12888543 | SAMN16539933 | 405381 | 380132 (93.77%) | 240819 (59.40%) | 91.3 | 72.76 |
SRR12888544 | SAMN16539932 | 826809 | 791728 (95.75%) | 508404 (61.48%) | 91.34 | 75.54 |
SRR12888545 | SAMN16539931 | 127318 | 118067 (92.73%) | 74319 (58.37%) | 91.34 | 72.41 |
SRR12888546 | SAMN16539930 | 388572 | 371639 (95.64%) | 242492 (62.40%) | 91.38 | 75.25 |
SRR12888547 | SAMN16539929 | 442756 | 424641 (95.90%) | 278546 (62.91%) | 91.46 | 75.11 |
SRR12888548 | SAMN16539928 | 563236 | 532363 (94.51%) | 340747 (60.49%) | 91.41 | 74.93 |
SRR12888549 | SAMN16539960 | 196027 | 186099 (94.93%) | 122736 (62.61%) | 91.5 | 75.22 |
SRR12888550 | SAMN16539959 | 327373 | 306881 (93.74%) | 196373 (59.98%) | 91.39 | 72.33 |
SRR12888551 | SAMN16539958 | 304931 | 285035 (93.47%) | 179615 (58.90%) | 91.25 | 71.96 |
SRR12888552 | SAMN16539957 | 513055 | 491096 (95.71%) | 314693 (61.33%) | 91.41 | 75.2 |
SRR12888553 | SAMN16539956 | 215282 | 206837 (96.07%) | 138239 (64.21%) | 91.51 | 75.65 |
SRR13267647 | SAMN09930639 | 24248 | 23903 (98.57%) | 18264 (75.32%) | 98.82 | 99.6 |
SRR13267648 | SAMN09930637 | 31923 | 31728 (99.38%) | 25776 (80.74%) | 99.11 | 99.52 |
SRR13267649 | SAMN09930639 | 305309 | 300937 (98.56%) | 223413 (73.17%) | 98.26 | 98.37 |
SRR13267650 | SAMN09930638 | 44885 | 42979 (95.75%) | 37780 (84.17%) | 99.32 | 99.54 |
SRR13267651 | SAMN09930637 | 33584 | 32606 (97.08%) | 28137 (83.78%) | 99.29 | 99.64 |
SRR13267652 | SAMN09930638 | 27220 | 27126 (99.65%) | 20516 (75.37%) | 98.93 | 99.21 |
SRR13267653 | SAMN09930638 | 31137 | 30787 (98.87%) | 25665 (82.42%) | 99.18 | 99.64 |
SRR13267654 | SAMN09930637 | 272921 | 269852 (98.87%) | 202456 (74.18%) | 98.52 | 98.66 |
SRR13267655 | SAMN09930638 | 261160 | 257223 (98.49%) | 179752 (68.82%) | 98.11 | 98.2 |
SRR13267656 | SAMN09930639 | 29831 | 29694 (99.54%) | 23541 (78.91%) | 99 | 99.45 |
SRR13267657 | SAMN09930640 | 31581 | 30305 (95.95%) | 25702 (81.38%) | 99.12 | 99.56 |
SRR13267658 | SAMN09930640 | 27695 | 27614 (99.70%) | 21848 (78.88%) | 98.94 | 99.31 |
SRR13267659 | SAMN09930640 | 323571 | 319247 (98.66%) | 239907 (74.14%) | 98.18 | 98.28 |
SRR13267660 | SAMN09930640 | 26604 | 26338 (99.00%) | 21077 (79.22%) | 98.94 | 99.56 |
SRR13267661 | SAMN09930637 | 30806 | 30664 (99.53%) | 23521 (76.35%) | 99.02 | 99.36 |
SRR13267662 | SAMN09930639 | 67632 | 65209 (96.41%) | 55920 (82.68%) | 99.18 | 99.46 |
Protein alignments
Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by ProSplign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|
Aves GenBank | 5,909 | 5,655 (95.70%) | 5,653 (95.67%) | 70.59% | 84.14% |
Aves known RefSeq (NP_) | 1,459 | 1,419 (97.26%) | 1,419 (97.26%) | 77.75% | 86.08% |
Same-species GenBank | 9,294 | 9,036 (97.22%) | 9,034 (97.20%) | 78.46% | 88.93% |
Same-species known RefSeq (NP_) | 8,464 | 8,376 (98.96%) | 8,374 (98.94%) | 82.48% | 87.81% |
Homo sapiens known RefSeq (NP_) | 62,922 | 54,473 (86.57%) | 54,251 (86.22%) | 71.06% | 77.06% |
Source | Number of sequences retrieved from Entrez | Number (%) of sequences aligned by ProSplign | Number (%) of sequences passed to Gnomon | Average % identity | Average % coverage |
---|---|---|---|---|---|
Aves GenBank | 5,909 | 5,729 (96.95%) | 5,728 (96.94%) | 72.12% | 83.13% |
Aves known RefSeq (NP_) | 1,459 | 1,420 (97.33%) | 1,418 (97.19%) | 78.05% | 86.17% |
Same-species GenBank | 9,294 | 9,040 (97.27%) | 9,034 (97.20%) | 79.57% | 89.39% |
Same-species known RefSeq (NP_) | 8,464 | 8,375 (98.95%) | 8,369 (98.88%) | 82.34% | 87.35% |
Homo sapiens known RefSeq (NP_) | 62,922 | 54,416 (86.48%) | 54,181 (86.11%) | 71.04% | 77.00% |
Assembly-assembly alignments of current to previous assembly
When the assembly changes between two rounds of annotation, genes in the current and the previous annotation are mapped to each other using the genomic alignments of the current assembly to the previous assembly so that gene identifiers can be preserved. The success of the remapping depends largely on how well the two assembly versions align to each other.
Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.
First Pass | Total |
---|---|
bGalGal1.pat.whiteleghornlayer.GRCg7w (Current) Coverage: 90.81% | bGalGal1.pat.whiteleghornlayer.GRCg7w (Current) Coverage: 91.20% |
bGalGal1.pat.whiteleghornlayer.GRCg7w (Previous) Coverage: 100.00% | bGalGal1.pat.whiteleghornlayer.GRCg7w (Previous) Coverage: 100.00% |
Percent Identity: 100.00% | Percent Identity: 99.97% |
Assembly-assembly alignments of alternate to reference assembly
When multiple assemblies of good quality are available for the organism, the annotation of all is done in coordination. The alternate assemblies are aligned to the reference assembly and the best reciprocal best hits are used to identify corresponding regions, that can then be annotated together.
Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.
First Pass | Total |
---|---|
bGalGal1.pat.whiteleghornlayer.GRCg7w (Alternate) Coverage: 97.83% | bGalGal1.pat.whiteleghornlayer.GRCg7w (Alternate) Coverage: 98.75% |
bGalGal1.mat.broiler.GRCg7b (Reference) Coverage: 97.46% | bGalGal1.mat.broiler.GRCg7b (Reference) Coverage: 98.41% |
Percent Identity: 99.26% | Percent Identity: 99.21% |
Comparison of the current and previous annotations
The annotation produced for this release (106) was compared to the annotation in the previous release (105) for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.). If the assembly was updated between the two releases, alignments between the current and the previous assembly were used to match the current and previous gene and transcript features in mapped regions.
The table below summarizes the changes in the gene set for each assembly as a percent of the number of genes in the current annotation release, and provides links to the details of the comparison in tabular format and in a Genome Workbench project.
bGalGal1.mat.broiler.GRCg7b (Current) to bGalGal1.mat.broiler.GRCg7b (Previous) | bGalGal1.pat.whiteleghornlayer.GRCg7w (Current) to bGalGal1.pat.whiteleghornlayer.GRCg7w (Previous) | |
---|---|---|
Identical | 20% | 17% |
Minor changes | 69% | 61% |
Major changes | 7% | 10% |
New | 4% | 11% |
Deprecated | 4% | 4% |
Other | <1% | 1% |
Download the report | tabular, Genome Workbench | tabular, Genome Workbench |
References
- RefSeq: Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, Dicuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Nucleic Acids Research 2014, 42(Database issue):D756-63
- BUSCO: Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM. Molecular biology and evolution 2021.38(10):4647-4654
- RepeatMasker: Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996–2004. http://www.repeatmasker.org
- WindowMasker: Morgulis A, Gertz EM, Schäffer AA, Agarwala R. Bioinformatics 2006, 2:134-41
- Splign: Kapustin Y, Souvorov A, Tatusova T, Lipman D. Biology Direct 2008, 3:20
- Minimap2: Li H. Bioinformatics 2018 Sep 15;34(18):3094-3100