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Susie_PABv2

Organism name:
Pongo abelii (Sumatran orangutan)
Isolate:
Susie
Sex:
female
BioSample:
SAMN06275555
BioProject:
PRJNA369439
Submitter:
University of Washington
Date:
2018/01/19
Synonyms:
ponAbe3
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_002880775.3 (latest)
RefSeq assembly accession:
GCF_002880775.1 (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:
NDHI03
Assembly method:
Falcon v. (git hash: 91e700c4) Nov 2015; BioNano Access Hybrid Scaffolds
Expected final version:
no
Genome coverage:
101.2x
Sequencing technology:
PacBio; Illumina NextSeq 500; BioNano Saphyr (two enzyme)

IDs: 1529631 [UID] 5907498 [GenBank] 6026018 [RefSeq]

See Genome Information for Pongo abelii

There are 3 assemblies for this organism

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History (Show revision history)

Comment

This is the whole-genome assembly of a female orangutan, Susie. Genome assembly was done in stages, incorporating data from multiple genomic platforms including PacBio, Illumina, and BioNano optical maps, resulting in three progressive versions:
V0 (GCA_002880775.1): The backbone of the ... assembly is made up of contigs obtained by assembling the PacBio (P6-C4 chemistry) reads using the Falcon assembler. These contigs are error-corrected using the tool Quiver and then further error-corrected using Pilon with 37-fold Illumina paired-end reads.
V1 (GCA_002880775.2): BioNano optical maps are used to place the contigs into scaffolds, followed by chromosome-level scaffolding using bicolor FISH.
V2 (GCA_002880775.3): The assembly is further error-corrected, particularly in regions that have clustered 1-2 bp indels. This is done by applying an Eichler-lab-created Freebayes-based indel correction method.  more

Global statistics

Total sequence length3,065,052,215
Total ungapped length3,043,444,524
Gaps between scaffolds39
Number of scaffolds5,300
Scaffold N5098,475,126
Scaffold L5013
Number of contigs5,814
Contig N5011,074,009
Contig L5083
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)5,814

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_002880785.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM009262.2=NC_036903.12
Chromosome 2ACM009263.2=NC_036904.11
Chromosome 2BCM009264.2=NC_036905.10
Chromosome 3CM009265.2=NC_036906.11
Chromosome 4CM009266.2=NC_036907.11
Chromosome 5CM009267.2=NC_036908.10
Chromosome 6CM009268.2=NC_036909.11
Chromosome 7CM009269.2=NC_036910.13
Chromosome 8CM009270.2=NC_036911.11
Chromosome 9CM009271.2=NC_036912.10
Chromosome 10CM009272.2=NC_036913.10
Chromosome 11CM009273.2=NC_036914.18
Chromosome 12CM009274.2=NC_036915.10
Chromosome 13CM009275.2=NC_036916.10
Chromosome 14CM009276.2=NC_036917.14
Chromosome 15CM009277.2=NC_036918.10
Chromosome 16CM009278.2=NC_036919.15
Chromosome 17CM009279.2=NC_036920.15
Chromosome 18CM009280.2=NC_036921.10
Chromosome 19CM009281.2=NC_036922.10
Chromosome 20CM009282.2=NC_036923.14
Chromosome 21CM009283.2=NC_036924.11
Chromosome 22CM009284.2=NC_036925.10
Chromosome XCM009285.2=NC_036926.19
unplacedn/an/an/a5,190

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule3,065,035,7165,2993,043,428,02598,475,12651439
Chromosome 1AllAssembled moleculeUnlocalized scaffolds227,986,559227,913,70472,855422226,878,416226,805,56172,855125,251,482125,251,48236,65444440110
Chromosome 2AAllAssembled moleculeUnlocalized scaffolds109,580,484109,511,69468,790651107,962,456107,893,66668,790101,897,474101,897,47468,79025250440
Chromosome 2BAssembled molecule129,937,8031129,884,686129,937,803200
Chromosome 3AllAssembled moleculeUnlocalized scaffolds196,656,042193,656,2552,999,787321196,124,743193,465,7362,659,007154,476,090154,476,0902,999,78727243110
Chromosome 4AllAssembled moleculeUnlocalized scaffolds189,403,205189,387,57215,633541188,637,138188,621,50515,633123,583,796123,583,79615,63327270330
Chromosome 5Assembled molecule179,185,8132178,894,089132,081,249161
Chromosome 6AllAssembled moleculeUnlocalized scaffolds169,560,327169,501,13659,191321169,298,457169,239,26659,191110,860,796110,860,79659,19124240110
Chromosome 7AllAssembled moleculeUnlocalized scaffolds155,186,585145,408,1059,778,480523153,605,206143,867,2769,737,930128,539,191128,539,1915,966,76035287110
Chromosome 8AllAssembled moleculeUnlocalized scaffolds144,055,422144,036,38819,034431143,253,405143,234,37119,03443,357,84043,357,84019,03418180220
Chromosome 9Assembled molecule112,206,1102111,893,977112,142,046101
Chromosome 10Assembled molecule132,178,4925131,736,72987,906,024284
Chromosome 11AllAssembled moleculeUnlocalized scaffolds128,683,459128,122,151561,308918128,048,964127,487,656561,308128,122,151128,122,151404,17221210000
Chromosome 12Assembled molecule132,184,0512131,861,482130,927,100151
Chromosome 13Assembled molecule98,475,126196,931,71298,475,126160
Chromosome 14AllAssembled moleculeUnlocalized scaffolds89,179,29788,963,417215,88051489,003,04188,787,161215,88088,963,41788,963,417116,67312120000
Chromosome 15Assembled molecule82,547,911179,895,88382,547,911240
Chromosome 16AllAssembled moleculeUnlocalized scaffolds77,740,22968,237,9899,502,240105576,368,41767,442,5218,925,89646,165,10246,165,1027,156,50828199440
Chromosome 17AllAssembled moleculeUnlocalized scaffolds79,469,77375,914,0073,555,76694577,211,63574,136,6933,074,94244,946,32644,946,3263,195,49319145330
Chromosome 18Assembled molecule75,923,960175,244,33175,923,96090
Chromosome 19Assembled molecule57,575,784356,795,31422,484,973312
Chromosome 20AllAssembled moleculeUnlocalized scaffolds61,049,49860,841,859207,63973460,281,85360,074,214207,63922,071,63022,071,63064,282880220
Chromosome 21AllAssembled moleculeUnlocalized scaffolds34,943,25734,683,425259,83232134,914,42534,654,593259,83221,773,81421,773,814259,832550110
Chromosome 22Assembled molecule35,308,119635,153,38325,836,094125
Chromosome XAllAssembled moleculeUnlocalized scaffolds154,909,616151,242,6933,666,9231239153,617,330150,052,0383,565,29255,924,63755,924,6373,293,40937316220
unplacedAssembled molecule211,108,7945,190209,930,95364,15130
MoleculeTotal
Length
Mitochondrion MT16,499
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