Trachurus trachurus

Atlantic horse mackerel

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank fTraTra1: GCA_905171665.2 fTraTra1: GCA_905171655.2
ENA fTraTra1: GCA_905171665.2 fTraTra1: GCA_905171655.2
UCSC Genome Browser fTraTra1: GCA_905171665.2 fTraTra1: GCA_905171655.2

metadata.yaml (view) (edit on github)
species:
  short_name: fTraTra
  name: Trachurus trachurus
  taxon_id: 36212
  common_name: Atlantic horse mackerel
  order:
    name: Carangiformes
  family:
    name: Carangidae
  individuals:
    - short_name: fTraTra1
      biosample_id: SAMEA7524396
      sex:
  genome_size:
  genome_size_method:
  project: [ vgp ]
CC BY-SA 4.0, Peter Southwood (wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR fTraTra1 138.52 Gbp 168.89x 248.0 GiB
PacBio HiFi (.bam) fTraTra1 41.31 Gbp 50.37x 25.6 GiB
10x fTraTra1 111.34 Gbp 135.75x 71.0 GiB
Arima fTraTra1 85.58 Gbp 104.34x 52.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.82 Gbp.
Last upload on 8 February 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fTraTra1 PacBio CLR 138.52 Gbp 168.89x 248.0 GiB
PacBio HiFi (.bam) 41.31 Gbp 50.37x 25.6 GiB
10x 111.34 Gbp 135.75x 71.0 GiB
Arima 85.58 Gbp 104.34x 52.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.82 Gbp.
Last upload on 8 February 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 16 December 2020
fTraTra1.pri.asm.20201216.fasta.gz (235.0 MiB)

Quality: 10.9 errors/Mb (QV=49.62)

Contigs Scaffolds
NG LG Len LG Len
10 4 17.80 Mbp 2 40.66 Mbp
20 8 15.98 Mbp 4 37.40 Mbp
30 15 10.02 Mbp 6 36.28 Mbp
40 24 8.13 Mbp 8 35.83 Mbp
50 36 6.26 Mbp 10 35.45 Mbp
60 50 5.23 Mbp 13 33.39 Mbp
70 68 4.00 Mbp 15 31.05 Mbp
80 91 3.02 Mbp 18 29.25 Mbp
90 128 1.63 Mbp 21 25.35 Mbp
100 453 11 bp 218 9.80 Kbp
1.000x 454 0.82 Gbp 219 0.82 Gbp
NG based on genome size 0.82 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 16 December 2020
fTraTra1.alt.asm.20201216.fasta.gz (235.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 15 3.91 Mbp 15 3.92 Mbp
20 39 3.10 Mbp 38 3.16 Mbp
30 68 2.48 Mbp 67 2.53 Mbp
40 105 2.06 Mbp 104 2.08 Mbp
50 152 1.55 Mbp 148 1.61 Mbp
60 213 1.20 Mbp 206 1.24 Mbp
70 294 0.84 Mbp 282 0.89 Mbp
80 410 0.59 Mbp 392 0.62 Mbp
90 587 346.69 Kbp 558 377.95 Kbp
100 1259 742 bp 1184 742 bp
1.000x 1260 0.82 Gbp 1185 0.82 Gbp
NG based on genome size 0.82 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 3 October 2019
fTraTra1.MT.20191003.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.