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Orenil1.1

Organism name:
Oreochromis niloticus
Isolate:
000638D3DF
Sex:
female
BioSample:
SAMN00117560
Submitter:
Broad Institute
Date:
2012/02/08
Synonyms:
oreNil2
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000188235.2 (latest)
RefSeq assembly accession:
GCF_000188235.2 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT.
Data displayed for RefSeq version
WGS Project:
AERX01
Assembly method:
AllPaths-LG v. R35292
Genome coverage:
269x
Sequencing technology:
Illumina

IDs: 354508 [UID] 354508 [GenBank] 768498 [RefSeq]

See Genome Information for Oreochromis niloticus

History (Show revision history)

Comment

The 01 contigs were updated in February 2011 to replace the IUPAC ambiguity bases present at SNP locations in the original sequences with a called base plus variation features for the other bases observed at that location during the ... assembly process. Therefore, many 01 contigs were updated to version .2, eg contig050015 is now AERX01050015.2
Sequenced and assembled at the Broad Institute. The sequenced animal is derived from a clonal line of tilapia fish and was provided by Dr. David Penman at the University of Stirling Institute of Agriculture, Stirling, UK. The RH map used to anchor this tilapia genome assembly was constructed by members of the Galibert, Baroilier and Ozouf laboratories  more

Global statistics

Total sequence length927,696,114
Total assembly gap length111,611,440
Gaps between scaffolds232
Number of scaffolds5,910
Scaffold N502,766,223
Number of contigs77,755
Contig N5029,493
Total number of chromosomes and plasmids23

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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_000188245.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Linkage Group LG1CM001444.1=NC_022199.10
Linkage Group LG2CM001445.1=NC_022200.10
Linkage Group LG3CM001446.1=NC_022201.10
Linkage Group LG4CM001447.1=NC_022202.10
Linkage Group LG5CM001448.1=NC_022203.10
Linkage Group LG6CM001449.1=NC_022204.10
Linkage Group LG7CM001450.1=NC_022205.10
Linkage Group LG8-24CM001451.1=NC_022206.10
Linkage Group LG9CM001452.1=NC_022207.10
Linkage Group LG10CM001453.1=NC_022208.10
Linkage Group LG11CM001454.1=NC_022209.10
Linkage Group LG12CM001455.1=NC_022210.10
Linkage Group LG13CM001456.1=NC_022211.10
Linkage Group LG14CM001457.1=NC_022212.10
Linkage Group LG15CM001458.1=NC_022213.10
Linkage Group LG16-21CM001459.1=NC_022214.10
Linkage Group LG17CM001460.1=NC_022215.10
Linkage Group LG18CM001461.1=NC_022216.10
Linkage Group LG19CM001462.1=NC_022217.10
Linkage Group LG20CM001463.1=NC_022218.10
Linkage Group LG22CM001464.1=NC_022219.10
Linkage Group LG23CM001465.1=NC_022220.10
unplacedn/an/an/a5,655

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Linkage Group LG131,194,787829,668,9246,443,2761,3807
Linkage Group LG225,048,291623,651,6304,585,3231,1415
Linkage Group LG319,325,3631417,116,4382,865,9441,32913
Linkage Group LG428,679,955925,726,5634,409,5491,9338
Linkage Group LG537,389,0891234,188,7583,817,5192,45511
Linkage Group LG636,725,2432133,595,9792,324,6082,28720
Linkage Group LG751,042,2561747,032,9027,306,5153,05916
Linkage Group LG8-2429,447,820927,015,4766,775,4051,7408
Linkage Group LG920,956,653619,941,7473,156,3228475
Linkage Group LG1017,092,887916,191,4722,801,8678668
Linkage Group LG1133,447,4721630,737,2772,768,2962,03315
Linkage Group LG1234,679,7061431,892,2053,660,0182,00613
Linkage Group LG1332,787,2611030,752,0775,633,6831,6319
Linkage Group LG1434,191,0231831,241,5222,766,2232,10417
Linkage Group LG1526,684,556924,913,6624,204,3281,4028
Linkage Group LG16-2134,890,0081631,793,9712,629,6582,29915
Linkage Group LG1731,749,9601229,354,6953,641,3181,93211
Linkage Group LG1826,198,306824,084,9263,899,8401,4697
Linkage Group LG1927,159,2521225,354,9503,775,8131,44111
Linkage Group LG2031,470,686928,866,5844,524,8681,8528
Linkage Group LG2226,410,4051324,217,9133,924,0791,57412
Linkage Group LG2320,779,993619,140,4265,141,9381,3335
unplaced270,328,5155,655209,587,950757,81533,7320
MoleculeTotal
Length
Mitochondrion MT16,627