Danio rerio

zebrafish

Included in the VGP.

- S3 File Index -- S3 Interactive Viewer -- NCBI Taxonomy Browser -


Resource Primary Assembly Alternate Assembly
GenBank fDanRer4: GCA_944039275.1 fDanRer4: GCA_944039255.1
ENA fDanRer4: GCA_944039275.1 fDanRer4: GCA_944039255.1
UCSC Genome Browser fDanRer4: GCA_944039275.1 fDanRer4: GCA_944039255.1

metadata.yaml (view) (edit on github)
species:
  short_name: fDanRer
  name: Danio rerio
  taxon_id: 29144
  common_name: zebrafish
  order:
    name: Cypriniformes
  family:
    name: Cyprinidae
  individuals:
    - short_name: fDreSAT1
      biosample_id: SAMEA104236293
      strain: SAT
      mother: fDreABH1
      father: fDreTuH1
    - short_name: fDreSAT3
      strain: SAT
    - short_name: fDreABH1
      biosample_id: SAMEA3891249
      strain: AB
      sex: male
      description: AB strain double haploid female founder of SAT strain 
    - short_name: fDreTuH1
      biosample_id: SAMEA3891248
      strain: Tuebingen
      sex: female
      description: Tuebingen strain double haploid female founder of SAT strain
  genome_size: 
  genome_size_method:
  project: [ vgp ]
CC BY-SA 2.0, Lynn Ketchum (wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fDanRer12 4468.83 Gbp N/A 7.5 TiB
PacBio HiFi (.fq) fDanRer12 276.16 Gbp N/A 254.0 GiB
PacBio HiFi (.bam) fDanRer12 279.04 Gbp N/A 1.0 TiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 January 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fDanRer12 PacBio HiFi (subreads) 4468.83 Gbp N/A 7.5 TiB
PacBio HiFi (.fq) 276.16 Gbp N/A 254.0 GiB
PacBio HiFi (.bam) 279.04 Gbp N/A 1.0 TiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 20 January 2024.
Assemblies
Individual 1 Maternal Assembly
Version assembly_curated from 22 May 2020
fDreSAT1.mat.cur.20200522.fasta.gz (387.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 12.11 Mbp 1 72.59 Mbp
20 22 8.09 Mbp 4 59.97 Mbp
30 42 5.79 Mbp 6 59.35 Mbp
40 68 4.64 Mbp 8 55.94 Mbp
50 102 3.59 Mbp 11 54.39 Mbp
60 143 2.91 Mbp 13 53.21 Mbp
70 198 2.10 Mbp 16 49.38 Mbp
80 278 1.39 Mbp 19 45.93 Mbp
90 425 0.55 Mbp 22 38.89 Mbp
100 2105 1.02 Kbp 753 1.02 Kbp
1.000x 2106 1.36 Gbp 754 1.36 Gbp
NG based on genome size .
Individual 1 Paternal Assembly
Version assembly_curated from 22 May 2020
fDreSAT1.pat.cur.20200522.fasta.gz (385.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 14.25 Mbp 1 62.61 Mbp
20 20 8.71 Mbp 4 57.66 Mbp
30 37 7.18 Mbp 6 56.54 Mbp
40 58 6.01 Mbp 9 54.75 Mbp
50 84 4.53 Mbp 11 52.96 Mbp
60 118 3.51 Mbp 14 50.01 Mbp
70 163 2.58 Mbp 16 49.74 Mbp
80 225 1.74 Mbp 19 46.41 Mbp
90 344 0.71 Mbp 22 39.02 Mbp
100 1963 1.02 Kbp 1251 1.02 Kbp
1.000x 1964 1.35 Gbp 1252 1.35 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 2 October 2019
fDreSAT1.MT.20191002.fasta.gz (5.0 KiB)

Quality: not computed
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.