Gasterosteus aculeatus

three-spined stickleback

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  short_name: fGasAcu
  name: Gasterosteus aculeatus
  taxon_id: 69293
  common_name: three-spined stickleback
  order:
    name: Gasterosteiformes
  family:
    name: Gasterosteidae
  individuals:
    - short_name: fGasAcu3
      biosample_id: SAMEA11296546
      sex: male
  genome_size: 625920000
  genome_size_method: GoaT
  project: [ vgp ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.bam) fGasAcu3 48.48 Gbp 77.46x 29.8 GiB
Arima fGasAcu3 80.01 Gbp 127.83x 25.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.63 Gbp.
Last upload on 19 June 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fGasAcu3 PacBio HiFi (.bam) 48.48 Gbp 77.46x 29.8 GiB
Arima 80.01 Gbp 127.83x 25.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.63 Gbp.
Last upload on 19 June 2023.
Assemblies
Individual 3 Primary Assembly
Version assembly_cambridge from 11 May 2023
fGasAcu3.pri.asm.20230511.fasta.gz (138.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 5.58 Mbp 2 32.52 Mbp
20 21 4.32 Mbp 5 24.02 Mbp
30 37 3.61 Mbp 7 23.28 Mbp
40 56 3.04 Mbp 10 21.85 Mbp
50 80 2.31 Mbp 13 20.37 Mbp
60 111 1.66 Mbp 16 18.66 Mbp
70 158 0.97 Mbp 20 17.01 Mbp
80 0 0
90 0 0
100 0 0
0.797x 328 498.83 Mbp 65 498.88 Mbp
NG based on genome size 0.63 Gbp.
Individual 3 Alternate Assembly
Version assembly_cambridge from 11 May 2023
fGasAcu3.alt.asm.20230511.fasta.gz (93.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 20 2.58 Mbp 20 2.58 Mbp
20 53 1.53 Mbp 53 1.53 Mbp
30 104 1.00 Mbp 104 1.00 Mbp
40 185 0.55 Mbp 185 0.55 Mbp
50 350 249.21 Kbp 350 249.21 Kbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.571x 900 357.60 Mbp 900 357.60 Mbp
NG based on genome size 0.63 Gbp.
Individual 3 Haplotype 1 Assembly
Version assembly_curated from 10 October 2024
fGasAcu3.hap1.cur.20241010.fasta.gz (142.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 5.89 Mbp 2 32.24 Mbp
20 22 4.12 Mbp 4 25.43 Mbp
30 39 3.22 Mbp 7 23.41 Mbp
40 61 2.57 Mbp 10 21.93 Mbp
50 88 2.07 Mbp 13 21.52 Mbp
60 124 1.46 Mbp 16 19.96 Mbp
70 178 0.91 Mbp 19 18.70 Mbp
80 318 196.19 Kbp 23 2.04 Mbp
90 0 0
100 0 0
0.817x 461 0.51 Gbp 130 0.51 Gbp
NG based on genome size 0.63 Gbp.
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 10 October 2024
fGasAcu3.hap2.cur.20241010.fasta.gz (127.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 5.30 Mbp 2 30.43 Mbp
20 23 3.75 Mbp 5 24.26 Mbp
30 42 2.90 Mbp 7 22.51 Mbp
40 67 2.27 Mbp 10 21.48 Mbp
50 99 1.58 Mbp 13 20.21 Mbp
60 149 0.94 Mbp 17 18.45 Mbp
70 265 284.00 Kbp 20 16.45 Mbp
80 0 0
90 0 0
100 0 0
0.731x 479 457.29 Mbp 170 457.35 Mbp
NG based on genome size 0.63 Gbp.
Individual 3 Mitochondrial Assembly
Version assembly_MT_cambridge from 20 September 2024
fGasAcu3.MT.20240920.fasta.gz (5.3 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.