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GRCz11

Description:
Genome Reference Consortium Zebrafish Build 11
Organism name:
Danio rerio (zebrafish)
Infraspecific name:
Strain: Tuebingen
BioSample:
SAMN06930106
BioProject:
PRJNA11776
Submitter:
Genome Reference Consortium
Date:
2017/05/09
Synonyms:
danRer11
Assembly type:
haploid-with-alt-loci
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
reference genome
GenBank assembly accession:
GCA_000002035.4 (latest)
RefSeq assembly accession:
GCF_000002035.6 (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

IDs: 1104621 [UID] 4482478 [GenBank] 4514068 [RefSeq]

See Genome Information for Danio rerio

There are 4 assemblies for this organism

See more

History (Show revision history)

Comment

The GRCz11 sequence is composed of genomic sequence, primarily finished clones that were sequenced as part of Zebrafish Genome Project at the Wellcome Trust Sanger Institute. PCR products and WGS shotgun sequence from mainly the WGS31 assembly (CABZ00000000.1) but ... also WGS29 (CAAK00000000.1) and WGS32 (CZQB00000000.1) have been added where necessary to fill gaps. In addition, unplaced sequences from WGS31 were added if they featured at least 5 kb of non-repetitive sequence, or if alignments with a cDNA could be detected that were not already covered by the placed sequences. For more information see: https://genomereference.org.  more

Global statistics

Number of regions with alternate loci or patches607
Total sequence length1,679,203,469
Total assembly gap length4,691,662
Gaps between scaffolds925
Number of scaffolds2,848
Scaffold N504,737,936
Scaffold L5071
Number of contigs20,680
Contig N50854,399
Contig L50358
Total number of chromosomes and plasmids26
Number of component sequences (WGS or clone)34,475

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
ALT_DRER_TU_1
ALT_DRER_TU_2
ALT_DRER_TU_3
ALT_DRER_TU_4
non-nuclear

Regions

NameLocation
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region40622:36792681-37013046
region40723:9241097-9599480
region40923:10092586-10620816
region41023:12290607-12563148
region41223:12926247-13652827
region41323:13678570-14310042
region41523:14524689-15416436
region41623:15555701-15967105
region41723:16025070-16143946
region41923:16417437-17219238
region42023:19155913-20029712
region42123:20277323-20618458
region42223:20959076-21423451
region42523:21483463-22850998
region42723:23077577-23613327
region42823:23660418-23990564
region42923:24371863-24720529
region43023:25075655-25329466
region43123:25571040-25882546
region43223:26769217-27220854
region43323:28054360-28680276
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region44224:4562163-4768192
region44324:11063433-11441034
region44424:11941761-12143729
region44524:12897992-13337309
region44624:13993676-14341924
region44724:18317648-18664575
region44824:20964707-21192435
region45224:21349106-22958100
region45324:23050323-23259308
region45424:23964964-24315023
region45524:25861513-26138014
region45624:27137984-27473843
region45724:27580084-27924588
region45824:28330083-28521863
region45924:28671516-28889580
region46024:31179275-31439902
region46124:32914442-33155428
region46224:37715878-38052109
region46324:40563952-40897722
region46425:2598978-2896658
region46525:8043471-8221931
region46625:10152702-10467523
region46725:11723503-11907858
region46925:12690698-13104582
region47125:13932353-14882274
region47225:15460371-15797733
region47325:17171754-17463109
region47425:18131907-18448764
region47525:19079967-19444984
region47625:20499207-20624036
region47925:20702241-22012693
region48125:22163402-22870363
region48325:23476227-24728543
region48425:27558927-28142834
region48525:28815575-28982194
Assembly Unit: Primary Assembly (GCF_000000175.5)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM002885.2=NC_007112.70
Chromosome 2CM002886.2=NC_007113.70
Chromosome 3CM002887.2=NC_007114.70
Chromosome 4CM002888.2=NC_007115.70
Chromosome 5CM002889.2=NC_007116.70
Chromosome 6CM002890.2=NC_007117.70
Chromosome 7CM002891.2=NC_007118.70
Chromosome 8CM002892.2=NC_007119.70
Chromosome 9CM002893.2=NC_007120.70
Chromosome 10CM002894.2=NC_007121.70
Chromosome 11CM002895.2=NC_007122.70
Chromosome 12CM002896.2=NC_007123.70
Chromosome 13CM002897.2=NC_007124.70
Chromosome 14CM002898.2=NC_007125.70
Chromosome 15CM002899.2=NC_007126.70
Chromosome 16CM002900.2=NC_007127.70
Chromosome 17CM002901.2=NC_007128.70
Chromosome 18CM002902.2=NC_007129.70
Chromosome 19CM002903.2=NC_007130.70
Chromosome 20CM002904.2=NC_007131.70
Chromosome 21CM002905.2=NC_007132.70
Chromosome 22CM002906.2=NC_007133.70
Chromosome 23CM002907.2=NC_007134.70
Chromosome 24CM002908.2=NC_007135.70
Chromosome 25CM002909.2=NC_007136.70
unplacedn/an/an/a967

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All1,373,454,7881,9171,368,765,5067,379,05317,811925
Chromosome 159,578,2823659,518,2044,818,34456135
Chromosome 259,640,6295559,561,1295,197,54074154
Chromosome 362,628,4893962,565,0974,572,48759438
Chromosome 478,093,7154975,268,6437,379,05344048
Chromosome 572,500,3767272,411,31013,500,41182471
Chromosome 660,270,0593660,194,4779,977,33572235
Chromosome 774,282,3995574,193,5855,009,32983554
Chromosome 854,304,6712854,255,7848,083,13846027
Chromosome 956,459,8462656,393,30832,000,14964225
Chromosome 1045,420,8673145,373,2674,706,89544630
Chromosome 1145,484,8374145,418,2837,242,23762640
Chromosome 1249,182,9543049,092,02732,399,08388129
Chromosome 1352,186,0273452,124,6028,482,59958233
Chromosome 1452,660,2322952,604,63228,653,34252828
Chromosome 1548,040,5782947,971,58129,777,15466328
Chromosome 1655,266,4843055,207,67214,334,44255929
Chromosome 1753,461,1004253,387,5905,946,31269541
Chromosome 1851,023,4782350,931,06115,551,65589722
Chromosome 1948,449,7713648,391,78411,329,99354535
Chromosome 2055,201,3324455,132,6619,260,50464543
Chromosome 2145,934,0664945,869,1234,066,63060348
Chromosome 2239,133,0802439,045,9255,145,64845423
Chromosome 2346,223,5843146,157,0413,380,09063530
Chromosome 2442,172,9263642,107,1724,737,93662235
Chromosome 2537,502,0514537,439,2054,876,66758444
unplaced28,352,95596728,150,34348,6722,0270
MoleculeTotal
Length
Mitochondrion MT16,596
Region
Name
LocationScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
region21:8535517-92857462690,331690,331385,5600
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region5214:10669008-110019771360,976360,976360,9760
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region5735:44586661-447569431174,280174,280174,2800
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Unit NameScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
ALT_DRER_TU_1749245,023,648245,021,468343,42122
ALT_DRER_TU_216354,631,56354,631,363358,3672
ALT_DRER_TU_3155,127,5705,127,570372,2420
ALT_DRER_TU_43949,304949,304370,6640
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