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Mmul_10

Organism name:
Macaca mulatta (Rhesus monkey)
Isolate:
AG07107
Sex:
female
BioSample:
SAMN09435472
BioProject:
PRJNA476474
Submitter:
The Genome Institute at Washington University School of Medicine
Date:
2019/02/13
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_003339765.3 (latest)
RefSeq assembly accession:
GCF_003339765.1 (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:
QNVO02

IDs: 2345051 [UID] 8740558 [GenBank] 8775378 [RefSeq]

See Genome Information for Macaca mulatta

There are 10 assemblies for this organism

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History (Show revision history)

Comment

The rhesus macaque (Macaca mulatta) DNA was derived from a fibroblast cell line (Coriell sample id: AG07107, MMU) of a single Indian origin female. The cell line was not transformed and taken at two years of age. Sequences were ... generated on the Pacific Biosciences RSII instrument (V2 chemistry) to approximately 66x genome coverage based on a genome size estimate of 3 Gb. All SMRT sequences were assembled with the HGAP4 algorithm (SMRT Link v5.0.1.9585) then error corrected using the Arrow error-correction module. Additional polishing of the assembly for residual indels was done by aligning 50x coverage of Illumina data and then running the Pilon algorithm. Finally, any residual indels were detected and corrected using a custom pipeline in the lab of Dr. Evan Eichler. All detected chimeric contigs were broken using a BioNano map as guidance, as well as the initial scaffolding process. Final chromosomal level scaffolds/contig files were generated by alignment to HiC data (Richard Green) and to the Mmul 8.0.1 reference. 
 Of the total sequence in scaffolds, 2,939,559,484 bp, in the assembled genome (Mmul_9.0), the assembly total contig number and N50 contig lengths are 3177 and 46.6 Mb (N=22), respectively. The total scaffold number and N50 scaffold lengths are 2975 and 82.3 Mb (N=14), respectively.
 Chromosome Y (CM003438) was added to Mmul_9.0, creating Mmul_10.
 For questions regarding the use of the Macaca mulatta Mmul_9.0 or Mmul_10 assembly please contact Dr. Wes Warren, Bond Life Sciences Center, University of Missouri, Columbia, MO; Dr. Evan Eichler, University of Washington, Seattle, WA or Tina Lindsay, McDonnell Genome Institute, Washington University, St Louis, MO. 
 Data use: The Macaca mulatta Mmul_9.0 and Mmul_10 assembly sequences are made available to the community by the McDonnell Genome Institute, Washington University, St Louis, MO with the following understanding: Users are free to analyze these data if the providers of this data are properly cited, any whole genome analyses should follow guidelines outlined in the Toronto agreement on the use of this assembly.
 Macaca mulatta Sequence and Assembly Credits: Sequencing Funds - This work was supported by the NHGRI grant No. 5U24HG00908103, HIGH QUALITY HUMAN AND NON-HUMAN PRIMATE GENOME ASSEMBLIES, at the McDonnell Genome Institute, Washington University School of Medicine DNA source - Coriell sample id: AG07107, MMU Genome Sequencing - The McDonnell Genome Institute, Washington University School of Medicine. Sequence Assembly - The McDonnell Genome Institute, Washington University School of Medicine. Sequence assembly curation - The McDonnell Genome Institute, Washington University School of Medicine; The University of Washington, Seattle, WA.  more

Global statistics

Total sequence length2,971,331,530
Total ungapped length2,936,892,733
Gaps between scaffolds41
Number of scaffolds2,979
Scaffold N5082,346,004
Scaffold L5014
Number of contigs3,182
Contig N5046,608,966
Contig L5022
Total number of chromosomes and plasmids23
Number of component sequences (WGS or clone)3,268

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_003339795.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM014336.1=NC_041754.121
Chromosome 2CM014337.1=NC_041755.110
Chromosome 3CM014338.1=NC_041756.120
Chromosome 4CM014339.1=NC_041757.117
Chromosome 5CM014340.1=NC_041758.115
Chromosome 6CM014341.1=NC_041759.114
Chromosome 7CM014342.1=NC_041760.118
Chromosome 8CM014343.1=NC_041761.117
Chromosome 9CM014344.1=NC_041762.115
Chromosome 10CM014345.1=NC_041763.114
Chromosome 11CM014346.1=NC_041764.114
Chromosome 12CM014347.1=NC_041765.17
Chromosome 13CM014348.1=NC_041766.17
Chromosome 14CM014349.1=NC_041767.118
Chromosome 15CM014350.1=NC_041768.114
Chromosome 16CM014351.1=NC_041769.116
Chromosome 17CM014352.1=NC_041770.119
Chromosome 18CM014353.1=NC_041771.17
Chromosome 19CM014354.1=NC_041772.120
Chromosome 20CM014355.1=NC_041773.14
Chromosome XCM014356.1=NC_041774.14
Chromosome YCM003438.1=NC_027914.10
unplacedn/an/an/a2,625

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,971,314,9662,9782,936,876,16982,346,00420341
Chromosome 1AllAssembled moleculeUnlocalized scaffolds224,851,259223,616,9421,234,31724321223,439,885222,205,5681,234,317135,966,267135,966,26755,58216160220
Chromosome 2AllAssembled moleculeUnlocalized scaffolds196,742,919196,197,964544,95512210195,405,478194,860,523544,955129,382,571129,382,57152,951880110
Chromosome 3AllAssembled moleculeUnlocalized scaffolds187,585,565185,288,9472,296,61823320186,478,801184,182,1832,296,618128,419,540128,419,5401,229,889550220
Chromosome 4AllAssembled moleculeUnlocalized scaffolds171,513,398169,963,0401,550,35819217170,050,971168,671,0111,379,960119,377,055119,377,05590,30211101110
Chromosome 5AllAssembled moleculeUnlocalized scaffolds188,135,706187,317,192818,51417215187,098,411186,279,897818,514103,971,188103,971,18856,442440110
Chromosome 6AllAssembled moleculeUnlocalized scaffolds179,867,432179,085,566781,86616214178,683,096177,901,230781,866131,468,112131,468,11261,300550110
Chromosome 7AllAssembled moleculeUnlocalized scaffolds170,859,803169,868,564991,23920218169,448,304168,457,065991,239108,982,702108,982,70261,44615150110
Chromosome 8AllAssembled moleculeUnlocalized scaffolds147,229,884145,679,3201,550,56419217144,671,758143,553,7081,118,05099,485,54099,485,540133,31213121110
Chromosome 9AllAssembled moleculeUnlocalized scaffolds135,000,623134,124,166876,45720515132,914,537132,038,080876,45790,864,71290,864,71264,64225250440
Chromosome 10AllAssembled moleculeUnlocalized scaffolds100,311,32799,517,758793,5691621496,914,40396,120,834793,56961,760,76161,760,76174,75117170110
Chromosome 11AllAssembled moleculeUnlocalized scaffolds133,773,592133,066,086707,50616214132,118,607131,411,101707,50695,136,37395,136,37365,186660110
Chromosome 12AllAssembled moleculeUnlocalized scaffolds130,293,451130,043,856249,595927129,184,372128,934,777249,595105,418,794105,418,79434,993550110
Chromosome 13AllAssembled moleculeUnlocalized scaffolds109,228,247108,737,130491,1171037108,188,855107,697,738491,11787,488,47987,488,47965,990440220
Chromosome 14AllAssembled moleculeUnlocalized scaffolds128,896,052128,056,306839,74623518127,835,032126,995,286839,74665,944,30065,944,30046,256550440
Chromosome 15AllAssembled moleculeUnlocalized scaffolds114,021,831113,283,604738,22717314111,294,234110,556,007738,22793,356,34793,356,34753,926770220
Chromosome 16AllAssembled moleculeUnlocalized scaffolds80,436,91079,627,064809,8462041678,645,14077,835,294809,84624,200,29424,200,29454,071770330
Chromosome 17AllAssembled moleculeUnlocalized scaffolds96,464,14895,433,4591,030,6892341995,061,49694,030,8071,030,68952,575,66452,575,66459,026880330
Chromosome 18AllAssembled moleculeUnlocalized scaffolds74,796,17274,474,043322,12992773,758,62273,436,493322,12947,509,38647,509,38641,974110110
Chromosome 19AllAssembled moleculeUnlocalized scaffolds60,612,13558,315,2332,296,9022332058,392,55056,383,0502,009,50024,310,52624,310,526134,43913112220
Chromosome 20AllAssembled moleculeUnlocalized scaffolds77,299,82577,137,495162,33062476,299,72576,137,395162,33045,648,50745,648,50736,919110110
Chromosome XAllAssembled moleculeUnlocalized scaffolds153,636,755153,388,924247,831844152,932,826152,684,995247,83159,398,40059,398,40068,99715150330
Chromosome YAssembled molecule11,753,682311,153,6827,945,85403
unplacedAssembled molecule98,004,2502,62596,905,38458,133120
MoleculeTotal
Length
Mitochondrion MT16,564
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