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sSteFas1.1

Organism name:
Stegostoma tigrinum (sharks & rays)
Isolate:
6-17
Sex:
female
BioSample:
SAMN18022887
BioProject:
PRJNA703743
Submitter:
Squalomix
Date:
2022/02/17
Assembly level:
Chromosome
Genome representation:
full
Excluded from RefSeq:
  • superseded by newer assembly for species
GenBank assembly accession:
GCA_022316705.1 (latest)
RefSeq assembly accession:
GCF_022316705.1 (suppressed) see latest RefSeq assembly for this species
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: 1 unlocalized scaffold on chromosome MT
  • Data displayed for GenBank version
WGS Project:
JAFIRC01
Assembly method:
Platanus v. 1.2.4; P_RNA_scaffolder v. commit 7941e0f on May 30, at github; 3D-DNA v. 180922
Expected final version:
yes
Genome coverage:
95.8x
Sequencing technology:
Illumina HiSeq

IDs: 12184081 [UID] 31912928 [GenBank] 33687648 [RefSeq]

See Genome Information for Stegostoma tigrinum

Pathogen Detection Resources

There are 3 assemblies for this organism

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History (Show revision history)

Comment

This assembly was assembled by the Platanus (v1.2.4) assembler using Illumina paired-end and mate-pair reads. The output scaffolds were used for RNA-seq read mapping, and a further scaffolding based on transcripts was performed with P_RNA_scaffolder (version: commit 7941e0f on ... May 30, at github). The resultant sequences were used for Hi-C read mapping, and a chromosome-scale scaffolding was performed with 3D-DNA (version: 180922). The final sequences 1 to 50 in the uploaded assembly file have chromosome-level connections. We define gaps of unknown length as 100bp and 500bp. The 100bp gaps indicate the gap connected by P_RNA_scaffolder (It is a scaffolding based on transcripts). And, the 500bp gaps indicate the gap connected by 3d-DNA (It is a scaffolding based on Hi-C).  more

Global statistics

Total sequence length2,771,882,974
Total ungapped length2,600,109,435
Gaps between scaffolds0
Number of scaffolds1,267
Scaffold N5076,588,082
Scaffold L5013
Number of contigs85,730
Contig N5056,707
Contig L5013,564
Total number of chromosomes and plasmids51
Number of component sequences (WGS or clone)1,267

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Assembly Information

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
non-nuclear
Assembly Unit: Primary Assembly (GCA_022316735.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM039227.1=NC_063384.10
Chromosome 2CM039228.1=NC_063385.10
Chromosome 3CM039229.1=NC_063386.10
Chromosome 4CM039230.1=NC_063387.10
Chromosome 5CM039231.1=NC_063388.10
Chromosome 6CM039232.1=NC_063389.10
Chromosome 7CM039233.1=NC_063390.10
Chromosome 8CM039234.1=NC_063391.10
Chromosome 9CM039235.1=NC_063392.10
Chromosome 10CM039236.1=NC_063393.10
Chromosome 11CM039237.1=NC_063394.10
Chromosome 12CM039238.1=NC_063395.10
Chromosome 13CM039239.1=NC_063396.10
Chromosome 14CM039240.1=NC_063397.10
Chromosome 15CM039241.1=NC_063398.10
Chromosome 16CM039242.1=NC_063399.10
Chromosome 17CM039243.1=NC_063400.10
Chromosome 18CM039244.1=NC_063401.10
Chromosome 19CM039245.1=NC_063402.10
Chromosome 20CM039246.1=NC_063403.10
Chromosome 21CM039247.1=NC_063404.10
Chromosome 22CM039248.1=NC_063405.10
Chromosome 23CM039249.1=NC_063406.10
Chromosome 24CM039250.1=NC_063407.10
Chromosome 25CM039251.1=NC_063408.10
Chromosome 26CM039252.1=NC_063409.10
Chromosome 27CM039253.1=NC_063410.10
Chromosome 28CM039254.1=NC_063411.10
Chromosome 29CM039255.1=NC_063412.10
Chromosome 30CM039256.1=NC_063413.10
Chromosome 31CM039257.1=NC_063414.10
Chromosome 32CM039258.1=NC_063415.10
Chromosome 33CM039259.1=NC_063416.10
Chromosome 34CM039260.1=NC_063417.10
Chromosome 35CM039261.1=NC_063418.10
Chromosome 36CM039262.1=NC_063419.10
Chromosome 37CM039263.1=NC_063420.10
Chromosome 38CM039264.1=NC_063421.10
Chromosome 39CM039265.1=NC_063422.10
Chromosome 40CM039266.1=NC_063423.10
Chromosome 41CM039267.1=NC_063424.10
Chromosome 42CM039268.1=NC_063425.10
Chromosome 43CM039269.1=NC_063426.10
Chromosome 44CM039270.1=NC_063427.10
Chromosome 45CM039271.1=NC_063428.10
Chromosome 46CM039272.1=NC_063429.10
Chromosome 47CM039273.1=NC_063430.10
Chromosome 48CM039274.1=NC_063431.10
Chromosome 49CM039275.1=NC_063432.10
Chromosome 50CM039276.1=NC_063433.10
unplacedn/an/an/a1,216

Assembly statistics

MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
All2,771,866,3161,2662,600,092,77776,588,08284,4630
Chromosome 1187,018,7871174,696,530187,018,7875,3570
Chromosome 2158,822,8651148,573,107158,822,8654,5550
Chromosome 3134,443,4071126,611,715134,443,4073,6620
Chromosome 4125,483,8491118,216,269125,483,8493,3400
Chromosome 5124,558,9731116,901,530124,558,9733,6080
Chromosome 6111,343,6801104,924,276111,343,6802,9090
Chromosome 7104,413,223197,892,317104,413,2232,9880
Chromosome 896,371,075190,946,00396,371,0752,6110
Chromosome 990,868,567185,497,25490,868,5672,5300
Chromosome 1084,264,930179,113,03784,264,9302,3520
Chromosome 1178,396,082173,389,14278,396,0822,2290
Chromosome 1276,759,553172,512,79676,759,5531,9480
Chromosome 1376,588,082172,414,11076,588,0821,8850
Chromosome 1472,754,116168,681,85972,754,1161,8630
Chromosome 1565,179,931161,742,30765,179,9311,7510
Chromosome 1665,111,622161,552,90665,111,6221,7230
Chromosome 1764,518,810160,819,81664,518,8101,7210
Chromosome 1861,678,605158,320,33261,678,6051,6390
Chromosome 1960,915,121157,348,71760,915,1211,7150
Chromosome 2055,334,592152,318,20755,334,5921,4790
Chromosome 2153,833,404150,708,84853,833,4041,4250
Chromosome 2253,258,631149,739,03553,258,6311,5350
Chromosome 2352,544,833149,760,23952,544,8331,3580
Chromosome 2450,948,696147,867,12450,948,6961,4760
Chromosome 2550,452,602147,548,70050,452,6021,4860
Chromosome 2646,925,174144,239,40046,925,1741,4060
Chromosome 2746,618,698143,994,83546,618,6981,2710
Chromosome 2843,502,945140,863,34143,502,9451,3050
Chromosome 2941,748,260139,558,50641,748,2601,1390
Chromosome 3040,741,570138,418,39940,741,5701,1130
Chromosome 3139,402,743137,347,05439,402,7431,1460
Chromosome 3238,506,508136,653,52338,506,5089730
Chromosome 3336,754,981134,668,61136,754,9819940
Chromosome 3428,151,094126,584,20428,151,0947870
Chromosome 3524,976,081122,770,24024,976,0811,0860
Chromosome 3624,930,835123,533,22824,930,8357770
Chromosome 3723,693,934121,945,70423,693,9348850
Chromosome 3822,198,511120,681,15922,198,5117930
Chromosome 3921,909,249120,162,16921,909,2498910
Chromosome 4017,419,972116,047,17217,419,9727690
Chromosome 4117,371,900115,873,39017,371,9001,0760
Chromosome 4213,957,721112,059,22413,957,7219500
Chromosome 4313,430,519111,924,41513,430,5198310
Chromosome 4412,713,090111,651,06812,713,0907700
Chromosome 4512,694,070111,124,08412,694,0708740
Chromosome 469,313,48117,873,4059,313,4818010
Chromosome 478,603,07317,227,3118,603,0738220
Chromosome 485,523,77614,760,3355,523,7763130
Chromosome 495,450,45514,396,5305,450,4559610
Chromosome 504,331,36613,935,9664,331,3663940
unplaced15,132,2741,21613,703,32818,5892,1910
MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
Mitochondrion MTAllAssembled moleculeUnlocalized scaffolds16,658016,65810116,658016,65816,658016,658000000