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Macaca_fascicularis_5.0

Organism name:
Macaca fascicularis (crab-eating macaque)
Sex:
female
BioSample:
SAMN00811240
Submitter:
Washington University (WashU)
Date:
2013/06/12
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000364345.1 (latest)
RefSeq assembly accession:
GCF_000364345.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT.
  • Data displayed for RefSeq version
WGS Project:
AQIA01
Assembly method:
SOAPdenovo v. 1.0.5, SRPRISM v. 2.4; ARGO v. 0.1
Genome coverage:
68x
Sequencing technology:
Illumina HiSeq

IDs: 704988 [UID] 704988 [GenBank] 779818 [RefSeq]

See Genome Information for Macaca fascicularis

There are 3 assemblies for this organism

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History (Show revision history)

Comment

Macaca fascicularis (cynomolgus macaque) Sequence Assembly Release Notes
 The cynomolgus macaque DNA for shotgun sequencing, is derived from a female, 5.8 yrs old, provided by Dr. Jay Kaplan and originated from "Tinjil", not a native location for cynomolgus, rather ... it is an island off the south coast of Java that was seeded with monkeys by the Washington National Primate Center. The original animal was trapped in eastern Sumatra. Sequences were generated on the Illumina HiSeq for assisted and de novo assembly. Sequence genome coverage for each paired end read type is as follows: 50x 300-500bp inserts, 10x 3kb insert and 2x 8kb insert. 
 Two independent assemblies were built with all sequence data, using an assisted assembler and the de novo assembler SOAP. The workflow for the assisted assembley is as follows: 1) map reads to reference and filter alignments using SRprism (unpublished but in process of being written up) that reports all alignments of equally good quality. Filtering is done by first finding out the histogram for per library insert size seen in alignments, deciding which range to use (usually tightest 99th percentile), and then retaining paired reads that have correct orientation with insert size in the desired range. Different data types (Illumina, traces, solid, 454) have slightly different filtering criteria. 2) use mapped and filtered reads for building consensus contigs. 3) find consecutive contigs that are bridged by mate pairs having 30-mers each on eith  more

Global statistics

Total sequence length2,946,843,737
Total assembly gap length142,977,039
Gaps between scaffolds24
Number of scaffolds7,625
Scaffold N5088,649,475
Scaffold L5014
Number of contigs87,764
Contig N5086,040
Contig L509,296
Total number of chromosomes and plasmids22

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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_000364355.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM001919.1=NC_022272.128
Chromosome 2CM001920.1=NC_022273.120
Chromosome 3CM001921.1=NC_022274.141
Chromosome 4CM001922.1=NC_022275.169
Chromosome 5CM001923.1=NC_022276.122
Chromosome 6CM001924.1=NC_022277.115
Chromosome 7CM001925.1=NC_022278.125
Chromosome 8CM001926.1=NC_022279.117
Chromosome 9CM001927.1=NC_022280.127
Chromosome 10CM001928.1=NC_022281.118
Chromosome 11CM001929.1=NC_022282.119
Chromosome 12CM001930.1=NC_022283.19
Chromosome 13CM001931.1=NC_022284.112
Chromosome 14CM001932.1=NC_022285.118
Chromosome 15CM001933.1=NC_022286.119
Chromosome 16CM001934.1=NC_022287.122
Chromosome 17CM001935.1=NC_022288.129
Chromosome 18CM001936.1=NC_022289.15
Chromosome 19CM001937.1=NC_022290.128
Chromosome 20CM001938.1=NC_022291.117
Chromosome XCM001939.1=NC_022292.112
unplacedn/an/an/a7,107

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,946,827,1627,6242,803,850,12388,649,47580,13924
Chromosome 1AllAssembled moleculeUnlocalized scaffolds228,955,476227,556,2641,399,21230228218,712,996217,433,3701,279,626138,665,737138,665,737152,5386,4726,365107110
Chromosome 2AllAssembled moleculeUnlocalized scaffolds192,909,870192,460,366449,50422220186,971,721186,559,336412,385125,741,623125,741,62363,0344,3104,27832110
Chromosome 3AllAssembled moleculeUnlocalized scaffolds193,512,962192,294,3771,218,58543241181,472,993180,410,8491,062,144129,674,376129,674,37664,8194,9314,831100110
Chromosome 4AllAssembled moleculeUnlocalized scaffolds173,232,586170,955,1032,277,48371269166,827,843164,881,2071,946,636119,724,987119,724,98765,3704,1403,886254110
Chromosome 5AllAssembled moleculeUnlocalized scaffolds190,271,649189,454,096817,55325322184,225,783183,527,297698,486105,597,079105,597,07987,6904,2194,13287220
Chromosome 6AllAssembled moleculeUnlocalized scaffolds181,913,984181,584,905329,07917215175,554,307175,247,550306,757132,081,036132,081,03674,6864,1974,17324110
Chromosome 7AllAssembled moleculeUnlocalized scaffolds172,638,558171,882,078756,48027225164,699,552164,071,319628,233107,376,033107,376,03353,0864,6574,58869110
Chromosome 8AllAssembled moleculeUnlocalized scaffolds147,524,517146,850,525673,99219217141,254,680140,657,447597,233100,378,728100,378,728423,5373,2203,16951110
Chromosome 9AllAssembled moleculeUnlocalized scaffolds133,925,568133,195,287730,28129227127,928,433127,272,501655,93292,187,01892,187,01846,6883,4043,35351110
Chromosome 10AllAssembled moleculeUnlocalized scaffolds96,855,22096,509,753345,4672021891,082,61290,761,517321,09560,750,29060,750,29027,3773,2213,19229110
Chromosome 11AllAssembled moleculeUnlocalized scaffolds138,871,270137,757,9261,113,34421219133,185,823132,144,0361,041,787101,971,489101,971,489603,9094,0373,97958110
Chromosome 12AllAssembled moleculeUnlocalized scaffolds132,992,465132,586,672405,7931239127,546,852127,191,125355,727106,729,359106,729,35970,3532,9172,88136220
Chromosome 13AllAssembled moleculeUnlocalized scaffolds111,518,885111,193,037325,84815312106,613,556106,335,528278,02888,649,47588,649,47575,8082,7872,74542220
Chromosome 14AllAssembled moleculeUnlocalized scaffolds132,195,074130,733,3711,461,70320218125,296,749123,895,4471,401,30267,271,94767,271,947992,5163,4133,36251110
Chromosome 15AllAssembled moleculeUnlocalized scaffolds113,086,136112,612,857473,27921219108,135,860107,712,928422,93298,078,25298,078,25257,6103,0442,99054110
Chromosome 16AllAssembled moleculeUnlocalized scaffolds82,009,34180,997,6211,011,7202422275,009,13174,103,573905,55857,635,53457,635,53490,8963,3133,22687110
Chromosome 17AllAssembled moleculeUnlocalized scaffolds97,546,54296,864,807681,7353122992,614,48892,008,008606,48053,877,09553,877,09547,9002,2932,22766110
Chromosome 18AllAssembled moleculeUnlocalized scaffolds75,807,05675,711,84795,20972571,849,47671,766,52782,94948,683,46848,683,46828,3241,6961,68511110
Chromosome 19AllAssembled moleculeUnlocalized scaffolds60,553,05359,248,2541,304,7993022852,581,05651,391,4991,189,55733,250,00333,250,00371,0523,7393,627112110
Chromosome 20AllAssembled moleculeUnlocalized scaffolds78,739,55578,541,002198,5531921772,565,36272,393,001172,36144,637,17144,637,17121,0822,6522,62428110
Chromosome XAllAssembled moleculeUnlocalized scaffolds153,601,299152,835,861765,43814212145,064,668144,357,465707,20393,731,72593,731,725214,3734,5314,48249110
unplacedAssembled molecule58,166,0967,10754,656,18222,4982,9460
MoleculeTotal
Length
Mitochondrion MT16,575
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