Genome assembly GRCz11
reference

FTP
Actions
NCBI RefSeq assembly
GCF_000002035.6
Submitted GenBank assembly
GCA_000002035.4
Taxon
Danio rerio (zebrafish)
Strain
Tuebingen
Synonym
danRer11
Assembly type
haploid with alt loci
Submitter
Genome Reference Consortium
Date
May 9, 2017

Assembly statistics

RefSeqGenBank
Genome size1.4 Gb1.4 Gb
Total ungapped length1.4 Gb1.4 Gb
Gaps between scaffolds925925
Number of chromosomes2525
Number of organelles10
Number of scaffolds1,9171,917
Scaffold N507.4 Mb7.4 Mb
Scaffold L504444
Number of contigs19,72519,725
Contig N501.4 Mb1.4 Mb
Contig L50219219
GC percent36.536.5
Assembly levelChromosomeChromosome
View sequencesview RefSeq sequencesview GenBank sequences

Sample details

BioSample ID
SAMN06930106
Description
Sample group for GRCz11
Submitter
Genome Reference Consortium
Strain
Tuebingen
Note
combined sample of SAMN03014687-SAMN03014693, SAMEA3146246, SAMEA3642453
SRA
ERS2108068
GenBank
GRCz11
Models
Generic
Package
Generic.1.0
Submission date
2017-05-11T15:30:03.223
Publication date
2017-05-11T00:00:00.000
Last updated
2017-09-30T00:32:18.060

Assembly methods

Comment

Assembly Name: GRCz11 Primary Assembly

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.

Additional genomes

Browse all Danio rerio genomes (19)

BioProject

PRJNA11776

Genome sequence for Danio rerio (zebrafish), currently maintained by the Genome Reference Consortium (GRC)

Annotation details

See full annotation report
RefSeq
ProviderNCBI RefSeq
NameGCF_000002035.6-RS_2024_08
DateAug 15, 2024
Genes46,466
Protein-coding27,158
Software version10.3

Quality analysis

BUSCO analysis (5.7.1)

C:98.4%[S:96.9%,D:1.5%],F:0.9%,M:0.6%,n:3640

actinopterygii_odb10 (3640)

Chromosomes

Chromosome
GenBank
RefSeq
Size (bp)
GC content (%)
Unlocalized count
Action
1CM002885.2NC_007112.759,578,28236.50
2CM002886.2NC_007113.759,640,62936.50
3CM002887.2NC_007114.762,628,489370
4CM002888.2NC_007115.778,093,715380
5CM002889.2NC_007116.772,500,37636.50
6CM002890.2NC_007117.760,270,05936.50
7CM002891.2NC_007118.774,282,39936.50
8CM002892.2NC_007119.754,304,67136.50
9CM002893.2NC_007120.756,459,84636.50
10CM002894.2NC_007121.745,420,86736.50
11CM002895.2NC_007122.745,484,83736.50
12CM002896.2NC_007123.749,182,95436.50
13CM002897.2NC_007124.752,186,02736.50
14CM002898.2NC_007125.752,660,23236.50
15CM002899.2NC_007126.748,040,578370
16CM002900.2NC_007127.755,266,48436.50
17CM002901.2NC_007128.753,461,10036.50
18CM002902.2NC_007129.751,023,47836.50
19CM002903.2NC_007130.748,449,77136.50
20CM002904.2NC_007131.755,201,33236.50
21CM002905.2NC_007132.745,934,06636.50
22CM002906.2NC_007133.739,133,080370
23CM002907.2NC_007134.746,223,584370
24CM002908.2NC_007135.742,172,92636.50
25CM002909.2NC_007136.737,502,05136.50
MTAC024175.3NC_002333.216,596400

Note: This genome assembly includes 967 unplaced scaffolds.

Revision history

GenBank
RefSeq
Name
Level
Date
Action
GCA_000002035.4GCF_000002035.6GRCz11ChromosomeMay 9, 2017
GCA_000002035.3GCF_000002035.5GRCz10ChromosomeSep 2, 2014
GCA_000002035.2GCF_000002035.4Zv9ChromosomeJul 15, 2010
GCA_000002035.1GCF_000002035.3Zv8ChromosomeJun 23, 2009
GCA_000002035.1GCF_000002035.2Zv8ChromosomeJun 23, 2009

n/a

GCF_000002035.1Zv7ChromosomeFeb 1, 2008