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fHypTra1

Organism name:
Hypomesus transpacificus (delta smelt)
Isolate:
Combined female
Sex:
female
BioSample:
SAMN24964577
BioProject:
PRJNA762373
Submitter:
Genomic Variation Lab at University of California Davis
Date:
2022/02/04
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_021917145.1 (latest)
RefSeq assembly accession:
GCF_021917145.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
JAJTOO01
Assembly method:
IPA v. 1.3.1; scaff10x v. 4.2; SALSA2 v. NA; Chromonomer v. 1.13
Expected final version:
yes
Genome coverage:
120.0x
Sequencing technology:
10X; PacBio Sequel; Hi-C

IDs: 11968301 [UID] 31495248 [GenBank] 32014118 [RefSeq]

See Genome Information for Hypomesus transpacificus

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The authors constructed this genome from two separate female samples. Sample isolates T1F02_BM_FF and T3F02_SC_FF were used in two different sequencing methods. T1F02_BM_FF was used to generate linked reads with Hi-C sequencing, while T3F02_SC_FF was used for long read ... sequencing. After sequencing, the data from both samples was used to create this assembly.  more

Global statistics

Total sequence length437,273,953
Total ungapped length436,919,854
Gaps between scaffolds0
Number of scaffolds376
Scaffold N5014,850,352
Scaffold L5013
Number of contigs1,850
Contig N50412,669
Contig L50267
Total number of chromosomes and plasmids26
Number of component sequences (WGS or clone)376

Supplemental Content

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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
Assembly Unit: Primary Assembly (GCF_021917595.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM038972.1=NC_061060.10
Chromosome 2CM038973.1=NC_061061.10
Chromosome 3CM038974.1=NC_061062.10
Chromosome 4CM038975.1=NC_061063.10
Chromosome 5CM038976.1=NC_061064.10
Chromosome 6CM038977.1=NC_061065.10
Chromosome 7CM038978.1=NC_061066.10
Chromosome 8CM038979.1=NC_061067.10
Chromosome 9CM038980.1=NC_061068.10
Chromosome 10CM038981.1=NC_061069.10
Chromosome 11CM038982.1=NC_061070.10
Chromosome 12CM038983.1=NC_061071.10
Chromosome 13CM038984.1=NC_061072.10
Chromosome 14CM038985.1=NC_061073.10
Chromosome 15CM038986.1=NC_061074.10
Chromosome 16CM038987.1=NC_061075.10
Chromosome 17CM038988.1=NC_061076.10
Chromosome 18CM038989.1=NC_061077.10
Chromosome 19CM038990.1=NC_061078.10
Chromosome 20CM038991.1=NC_061079.10
Chromosome 21CM038992.1=NC_061080.10
Chromosome 22CM038993.1=NC_061081.10
Chromosome 23CM038994.1=NC_061082.10
Chromosome 24CM038995.1=NC_061083.10
Chromosome 25CM038996.1=NC_061084.10
Chromosome 26CM038997.1=NC_061085.10
unplacedn/an/an/a350

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All437,273,953376436,919,85414,850,3521,4740
Chromosome 112,516,727112,505,82712,516,727370
Chromosome 217,206,656117,191,13317,206,656480
Chromosome 315,692,960115,681,46015,692,960590
Chromosome 411,481,881111,473,74711,481,881490
Chromosome 57,446,23717,437,2377,446,237300
Chromosome 615,113,095115,099,49515,113,095600
Chromosome 710,240,637110,232,33710,240,637470
Chromosome 814,090,550114,080,52714,090,550570
Chromosome 922,675,904122,658,25822,675,904740
Chromosome 1014,312,355114,299,35514,312,355540
Chromosome 1119,684,503119,668,08019,684,503650
Chromosome 1210,948,312110,932,38910,948,312560
Chromosome 1314,850,352114,841,15214,850,352400
Chromosome 1417,823,525117,812,52517,823,525540
Chromosome 1514,998,720114,982,32014,998,720560
Chromosome 167,741,04617,733,2467,741,046380
Chromosome 1717,325,139117,307,03917,325,139690
Chromosome 1814,953,238114,938,03814,953,238560
Chromosome 1915,775,655115,764,48915,775,655590
Chromosome 205,112,51815,109,9955,112,518180
Chromosome 2110,662,977110,655,77710,662,977400
Chromosome 2215,067,536115,051,23615,067,536710
Chromosome 2321,529,172121,513,97221,529,172760
Chromosome 246,043,78516,037,7856,043,785320
Chromosome 256,411,54016,404,4406,411,540190
Chromosome 269,256,48619,249,4869,256,486180
unplaced88,312,44735088,258,509583,3251920