Alosa sapidissima

American shad

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank fAloSap1: GCA_018492685.1 fAloSap1: GCA_018492705.1
ENA fAloSap1: GCA_018492685.1 fAloSap1: GCA_018492705.1
UCSC Genome Browser fAloSap1: GCA_018492685.1 fAloSap1: GCA_018492705.1

metadata.yaml (view) (edit on github)
species:
  short_name: fAloSap
  name: Alosa sapidissima
  taxon_id: 34773
  common_name: American shad
  order:
    name: Clupeiformes
  family:
    name: Clupeidae
  individuals:
    - short_name: fAloSap1
      sex: male
      provider: Reid Hyle, Nina Overgaard Therkildsen
    - short_name: fAloSap2
      sex: male
      provider: Reid Hyle, Nina Overgaard Therkildsen
  genome_size: 900000000
  genome_size_method:
  project: [ vgp ]
CC0 Raver Duane (Pixnio)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) fAloSap1 664.38 Gbp 738.19x 1.2 TiB
PacBio HiFi (.fq, Q≥20) fAloSap1 0.00x 23.0 GiB
Bionano fAloSap1 N/A 967.22x 1.6 GiB
Arima fAloSap1 99.47 Gbp 110.52x 67.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.90 Gbp.
Last upload on 25 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fAloSap1 PacBio HiFi (subreads) 664.38 Gbp 738.19x 1.2 TiB
PacBio HiFi (.fq, Q≥20) 0.00x 23.0 GiB
Bionano N/A 967.22x 1.6 GiB
Arima 99.47 Gbp 110.52x 67.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.90 Gbp.
Last upload on 25 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 21 April 2021
fAloSap1.pri.cur.20210421.fasta.gz (249.8 MiB)

Quality: 4.7 errors/Mb (QV=53.27)

Contigs Scaffolds
NG LG Len LG Len
10 14 4.46 Mbp 1 44.39 Mbp
20 39 3.21 Mbp 3 40.36 Mbp
30 70 2.44 Mbp 6 39.35 Mbp
40 112 1.92 Mbp 8 38.59 Mbp
50 165 1.55 Mbp 10 38.44 Mbp
60 231 1.19 Mbp 13 36.83 Mbp
70 323 0.83 Mbp 15 35.20 Mbp
80 456 0.54 Mbp 18 32.25 Mbp
90 690 264.79 Kbp 21 31.74 Mbp
100 0 29 269.70 Kbp
0.998x 1712 0.90 Gbp 73 0.90 Gbp
NG based on genome size 0.90 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 21 April 2021
fAloSap1.alt.cur.20210421.fasta.gz (239.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 58 1.03 Mbp 58 1.03 Mbp
20 162 0.73 Mbp 162 0.73 Mbp
30 307 0.55 Mbp 307 0.55 Mbp
40 492 432.32 Kbp 492 432.32 Kbp
50 729 333.03 Kbp 729 333.03 Kbp
60 1046 238.30 Kbp 1046 238.30 Kbp
70 1494 164.07 Kbp 1494 164.07 Kbp
80 2192 97.06 Kbp 2192 97.06 Kbp
90 3639 36.79 Kbp 3639 36.79 Kbp
100 0 0
0.947x 5411 0.85 Gbp 5410 0.85 Gbp
NG based on genome size 0.90 Gbp.
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.