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Sscrofa11.1

Description:
Sscrofa11 with Y sequences from WTSI_X_Y_pig V2
Organism name:
Sus scrofa (pig)
Infraspecific name:
Breed: Duroc
Isolate:
TJ Tabasco
Sex:
female
BioSample:
SAMN02953785
BioProject:
PRJNA13421
Submitter:
The Swine Genome Sequencing Consortium (SGSC)
Date:
2017/02/07
Synonyms:
susScr11
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000003025.6 (latest)
RefSeq assembly accession:
GCF_000003025.6 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
AEMK02
Assembly method:
Falcon v. OCT-2015
Expected final version:
yes
Genome coverage:
65.0x
Sequencing technology:
PacBio

IDs: 1004191 [UID] 4121818 [GenBank] 4192498 [RefSeq]

See Genome Information for Sus scrofa

There are 16 assemblies for this organism

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History (Show revision history)

Comment

This pig genome sequence (Sscrofa11) has been released by the International Swine Genome Sequencing Consortium under the terms of the Toronto Statement (Nature 2009, 461: 168). The Consortium is coordinating genome-wide analysis, annotation and publication. 
The sequence data from ... which this assembly was constructed largely comprise 65x genome coverage in whole genome shotgun (WGS) Pacific Biosciences long reads (Pacific Biosciences RSII, with P6/C4 chemistry). Illumina HiSeq2500 WGS paired-end and mate pair reads were used for final error correction using PILON. Sanger and Oxford Nanopore sequence data from a few CHORI-242 BAC clones were used to fill gaps. All the WGS data were generated from a single Duroc female (TJ Tabasco, also known as Duroc 2-14) which was also the source of DNA for the CHORI-BAC library. 
Sscrofa11 replaces the previous assembly, Sscrofa10.2, which was largely established from the same Duroc 2-14 DNA source.  more

Global statistics

Number of regions with alternate loci or patches2
Total sequence length2,501,912,388
Total assembly gap length29,864,641
Gaps between scaffolds93
Number of scaffolds706
Scaffold N5088,231,837
Scaffold L509
Number of contigs1,118
Contig N5048,231,277
Contig L5015
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)1,308

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

Regions

NameLocation
PARX:1029482-6405430
PARY:200470-4791971
Assembly Unit: Primary Assembly (GCF_000000215.6)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000812.5=NC_010443.50
Chromosome 2CM000813.5=NC_010444.40
Chromosome 3CM000814.5=NC_010445.40
Chromosome 4CM000815.5=NC_010446.50
Chromosome 5CM000816.5=NC_010447.50
Chromosome 6CM000817.5=NC_010448.40
Chromosome 7CM000818.5=NC_010449.50
Chromosome 8CM000819.5=NC_010450.40
Chromosome 9CM000820.5=NC_010451.40
Chromosome 10CM000821.5=NC_010452.40
Chromosome 11CM000822.5=NC_010453.50
Chromosome 12CM000823.5=NC_010454.40
Chromosome 13CM000824.5=NC_010455.50
Chromosome 14CM000825.5=NC_010456.50
Chromosome 15CM000826.5=NC_010457.50
Chromosome 16CM000827.5=NC_010458.40
Chromosome 17CM000828.5=NC_010459.50
Chromosome 18CM000829.5=NC_010460.40
Chromosome XCM000830.5=NC_010461.50
Chromosome YLT634572.1=NC_010462.39
unplacedn/an/an/a583

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,501,895,7757052,472,031,13488,231,83741393
Chromosome 1Assembled molecule274,330,5321274,330,132274,330,53240
Chromosome 2Assembled molecule151,935,9943151,800,670101,393,61842
Chromosome 3Assembled molecule132,848,9135132,648,51389,221,08344
Chromosome 4Assembled molecule130,910,9151130,870,669130,910,91530
Chromosome 5Assembled molecule104,526,0074104,375,10764,647,44493
Chromosome 6Assembled molecule170,843,5874170,419,461107,611,64473
Chromosome 7Assembled molecule121,844,0993121,743,19974,672,20292
Chromosome 8Assembled molecule138,966,2373138,865,93784,310,84332
Chromosome 9Assembled molecule139,512,0831139,511,883139,512,08320
Chromosome 10Assembled molecule69,359,453269,257,33344,332,88921
Chromosome 11Assembled molecule79,169,978279,119,67843,299,27331
Chromosome 12Assembled molecule61,602,749161,500,12861,602,74930
Chromosome 13Assembled molecule208,334,5901208,234,567208,334,590100
Chromosome 14Assembled molecule141,755,4461141,755,246141,755,44620
Chromosome 15Assembled molecule140,412,7252140,362,52588,231,83721
Chromosome 16Assembled molecule79,944,280179,944,28079,944,28000
Chromosome 17Assembled molecule63,494,081463,343,68148,466,28143
Chromosome 18Assembled molecule55,982,971155,982,97155,982,97100
Chromosome XAssembled molecule125,939,5953125,778,90165,063,12082
Chromosome YAllAssembled moleculeUnlocalized scaffolds45,127,33043,547,8281,579,5027970917,132,04315,568,3411,563,70212,044,92412,044,924438,7693343231169690
unplacedAssembled molecule65,054,21058365,054,210250,08100
MoleculeTotal
Length
Mitochondrion MT16,613
Region
Name
LocationScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
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