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Mmul_8.0.1

Organism name:
Macaca mulatta (Rhesus monkey)
Isolate:
17573
Sex:
female
BioProject:
PRJNA214746
Submitter:
Baylor College of Medicine Genome Sequencing Center
Date:
2015/11/30
Synonyms:
rheMac8
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000772875.3 (latest)
RefSeq assembly accession:
GCF_000772875.2 (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:
JSUE03
Genome coverage:
47.4x

IDs: 588981 [UID] 2701138 [GenBank] 2715158 [RefSeq]

See Genome Information for Macaca mulatta

There are 7 assemblies for this organism

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History (Show revision history)

Comment

The rhesus monkey that provided DNA for the project is ID 17573, a female from the Southwest National Primate Research Center at the Southwest Foundation for Biomedical Research in San Antonio, TX who was born Dec. 21, 1990 in ... San Antonio and died Jan. 25, 2002. All animals in that branch of the colony are derived from Indian origin rhesus brought to the US many years ago. This animal is not likely to be closely related to the Indian origin animal that provided DNA for the BAC library.
Beginning with the chromosomes from the 01 version of JSUE00000000, we used PBJelly to fill in gaps with PacBio reads. From the resulting sequences, we created 47130 contigs and an AGP file that describes the order and orientation of the contigs within the chromosomes. The remaining 301,360 contigs are the unplaced contigs from the 01 version, with contamination having been removed from 14 of them.
The chromosomes were renamed to the conventional Macaca mulatta chromosome names in the 02 version of JSUE00000000, assembly Mmul_8.0, and the conventional naming was maintained in later versions. The mapping of chromosome numbers is shown here. The .1 version of the chromosome accession numbers have the names shown in the MacaM_Assembly_v7 column (from the Zimin et al. paper), and the accession versions that are .2 and above have the names in column Mmul_8.0:

Mmul_8.0 MacaM_Assembly_v7 Accession
-------------------------------------------
1 1 CM002977
13 2a CM002978
12 2b CM002979
2 3 CM002980
5 4 CM002981
6 5 CM002982
4 6 CM002983
3 7 CM002984
8 8 CM002985
15 9 CM002986
9 10 CM002987
14 11 CM002988
11 12 CM002989
17 13 CM002990
7 14 CM002991
10 15 CM002992
20 16 CM002993
16 17 CM002994
18 18 CM002995
19 19 CM002996
X X CM002997

The BAC-based chromosome Y, accession CM003438, is also part of assembly Mmul_8.0 and above  more

Global statistics

Total sequence length3,236,224,332
Total ungapped length3,142,093,174
Gaps between scaffolds1,536
Number of scaffolds286,263
Scaffold N504,193,270
Scaffold L50202
Number of contigs348,494
Contig N50107,156
Contig L508,043
Total number of chromosomes and plasmids23
Number of component sequences (WGS or clone)348,580

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_000772885.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM002977.3=NC_027893.10
Chromosome 2CM002980.3=NC_027894.10
Chromosome 3CM002984.2=NC_027895.10
Chromosome 4CM002983.2=NC_027896.10
Chromosome 5CM002981.2=NC_027897.10
Chromosome 6CM002982.3=NC_027898.10
Chromosome 7CM002991.3=NC_027899.10
Chromosome 8CM002985.3=NC_027900.10
Chromosome 9CM002987.3=NC_027901.10
Chromosome 10CM002992.3=NC_027902.10
Chromosome 11CM002989.3=NC_027903.10
Chromosome 12CM002979.2=NC_027904.10
Chromosome 13CM002978.2=NC_027905.10
Chromosome 14CM002988.2=NC_027906.10
Chromosome 15CM002986.2=NC_027907.10
Chromosome 16CM002994.2=NC_027908.10
Chromosome 17CM002990.2=NC_027909.10
Chromosome 18CM002995.2=NC_027910.10
Chromosome 19CM002996.3=NC_027911.10
Chromosome 20CM002993.2=NC_027912.10
Chromosome XCM002997.3=NC_027913.10
Chromosome YCM003438.1=NC_027914.10
unplacedn/an/an/a284,705

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All3,236,207,768286,2623,142,076,6104,193,27062,2311,536
Chromosome 1225,584,828102220,126,8255,785,4663,786101
Chromosome 2204,787,37379199,561,1477,089,4572,78878
Chromosome 3185,818,99797181,066,9224,808,1023,05396
Chromosome 4172,585,72078167,673,4329,091,8762,51577
Chromosome 5190,429,64663184,750,3375,887,7432,48162
Chromosome 6180,051,39265175,378,4554,354,4822,43864
Chromosome 7169,600,52095165,645,3104,272,0522,82594
Chromosome 8144,306,98269140,526,7638,528,6111,96868
Chromosome 9129,882,84968126,827,1753,921,9671,89767
Chromosome 1092,844,0885891,140,8874,193,2701,94257
Chromosome 11133,663,16963129,728,6884,838,0942,38162
Chromosome 12125,506,78449121,776,7538,593,2431,65248
Chromosome 13108,979,91848106,626,8483,074,6541,70147
Chromosome 14127,894,41251124,775,7947,619,4171,89850
Chromosome 15111,343,17362108,925,1206,110,8441,84761
Chromosome 1677,216,7815075,181,8252,695,5172,01749
Chromosome 1795,684,4729593,015,25513,336,6941,30494
Chromosome 1870,235,4512368,466,9705,966,03588922
Chromosome 1953,671,03210652,205,7831,295,4342,357105
Chromosome 2074,971,4815473,224,3192,887,1621,54653
Chromosome X149,150,640179145,684,6462,124,3552,291178
Chromosome Y11,753,682311,153,6827,945,85403
unplaced400,244,378284,705378,613,6741,37416,6550
MoleculeTotal
Length
Mitochondrion MT16,564
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