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Sscrofa10.2

Organism name:
Sus scrofa
Infraspecific name:
Breed: Duroc
Isolate:
TJ Tabasco
Sex:
female
BioSample:
SAMN02953785
Submitter:
The Swine Genome Sequencing Consortium (SGSC)
Date:
2011/09/07
Synonyms:
susScr3
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000003025.4 (latest)
RefSeq assembly accession:
GCF_000003025.5 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT.
Data displayed for RefSeq version
WGS Project:
AEMK01
Assembly method:
SOAPdenovo v. 2.20 and Cortex v. 1.1
Genome coverage:
24x
Sequencing technology:
Illumina GAII

IDs: 304498 [UID] 302628 [GenBank] 304498 [RefSeq]

See Genome Information for Sus scrofa

There are 3 assemblies for this organism

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History (Show revision history)

Comment

This draft pig genome sequence (Sscrofa10.2) has been released by the International Swine Genome Sequencing Consortium under the terms of the Toronto Statement (Nature 2009, 461: 168). Sscrofa10.2 replaces the previous assembly, Sscrofa10, which had assembly errors. The International ... Swine Genome Sequencing Consortium is coordinating genome-wide analyses, as described in BMC Genomics 2010 11:438. Funders of the pig genome project are acknowledged in this marker paper.
The sequence data, from which this assembly was constructed, comprise hierarchical shotgun sequence data providing 4-6x genome coverage from BAC clones representing a minimal tile path across the genome plus >30x genome coverage in whole genome shotgun sequence (WGS) Illumina reads. All the WGS data and most of the BAC data are derived from blood cells of a single Duroc female pig (Duroc 2-14; CHORI-242 BAC library) but also includes some data from other BAC libraries from other breeds.
The chromosomes are CM000812-CM00830 and CM001155. They are built from 5343 placed scaffolds whose accessions are in the ranges GL878569-GL882503 and JH114391-JH118402. The 4562 unplaced scaffolds of Sscrofa10.2 have accessions in the ranges GL892100-GL896682 and JH118403-JH118999. Note that scaffolds in the previous assembly that are not in the current assembly have been suppressed.  more

Global statistics

Total sequence length2,808,525,991
Total assembly gap length289,397,178
Gaps between scaffolds5,323
Number of scaffolds9,906
Scaffold N50576,008
Number of contigs243,033
Contig N5069,474
Total number of chromosomes and plasmids21

Supplemental Content

PubMed articles for this assembly

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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 (GCF_000000215.5)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000812.4=NC_010443.40
Chromosome 2CM000813.4=NC_010444.30
Chromosome 3CM000814.4=NC_010445.30
Chromosome 4CM000815.4=NC_010446.40
Chromosome 5CM000816.4=NC_010447.40
Chromosome 6CM000817.4=NC_010448.30
Chromosome 7CM000818.4=NC_010449.40
Chromosome 8CM000819.4=NC_010450.30
Chromosome 9CM000820.4=NC_010451.30
Chromosome 10CM000821.4=NC_010452.30
Chromosome 11CM000822.4=NC_010453.40
Chromosome 12CM000823.4=NC_010454.30
Chromosome 13CM000824.4=NC_010455.40
Chromosome 14CM000825.4=NC_010456.40
Chromosome 15CM000826.4=NC_010457.40
Chromosome 16CM000827.4=NC_010458.30
Chromosome 17CM000828.4=NC_010459.40
Chromosome 18CM000829.4=NC_010460.30
Chromosome XCM000830.4=NC_010461.40
Chromosome YCM001155.2=NC_010462.20
unplacedn/an/an/a4,562

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Chromosome 1315,321,322692279,914,422562,3668,569691
Chromosome 2162,569,375331145,631,175692,9394,382330
Chromosome 3144,787,322304129,207,922654,3074,294303
Chromosome 4143,465,943276129,362,743715,8153,532275
Chromosome 5111,506,44123999,275,441618,1653,310238
Chromosome 6157,765,593366139,069,593529,8844,460365
Chromosome 7134,764,511266121,271,311712,5052,432265
Chromosome 8148,491,826309132,692,726573,2313,991308
Chromosome 9153,670,197276139,490,897713,3664,293275
Chromosome 1079,102,37315671,122,273628,0802,301155
Chromosome 1187,690,58119077,960,681555,4812,799189
Chromosome 1263,588,57114156,400,871543,6191,877140
Chromosome 13218,635,234449195,589,234629,7096,460448
Chromosome 14153,851,969259140,665,969807,0322,860258
Chromosome 15157,681,621332140,675,921617,4354,557331
Chromosome 1686,898,99116078,720,191743,2052,288159
Chromosome 1769,701,58114862,138,581638,7232,130147
Chromosome 1861,220,07110955,640,371813,9031,797108
Chromosome X144,288,218333127,507,118584,7901,811332
Chromosome Y1,637,71671,333,916207,906386
unplaced211,869,9224,562195,490,32298,022163,7960
MoleculeTotal
Length
Mitochondrion MT16,613