Scatophagus argus

spotted scat

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank fScaArg1: GCA_020382885.1 fScaArg1: GCA_020382915.1
ENA fScaArg1: GCA_020382885.1 fScaArg1: GCA_020382915.1
UCSC Genome Browser fScaArg1: GCA_020382885.1 fScaArg1: GCA_020382915.1

metadata.yaml (view) (edit on github)
species:
  common_name: spotted scat
  family:
    name: Scatophagidae
  genome_size: 647966298
  genome_size_method: genomescope
  individuals:
  - short_name: fScaArg1
  name: Scatophagus argus
  order:
    name: Perciformes
  short_name: fScaArg
  taxon_id: 75038
  project: [ vgp ]
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR fScaArg1 59.86 Gbp 92.38x 105.3 GiB
10x fScaArg1 72.88 Gbp 112.47x 36.6 GiB
Bionano fScaArg1 N/A 1425.77x 1.3 GiB
Arima fScaArg1 134.89 Gbp 208.17x 78.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.65 Gbp.
Last upload on 3 April 2020.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fScaArg1 PacBio CLR 59.86 Gbp 92.38x 105.3 GiB
10x 72.88 Gbp 112.47x 36.6 GiB
Bionano N/A 1425.77x 1.3 GiB
Arima 134.89 Gbp 208.17x 78.0 GiB
Bases and Coverage are approximate.
Coverage based on genome size 0.65 Gbp.
Last upload on 3 April 2020.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 16 July 2021
fScaArg1.pri.cur.20210716.fasta.gz (166.7 MiB)

Quality: 2.2 errors/Mb (QV=56.47)

Contigs Scaffolds
NG LG Len LG Len
10 2 25.15 Mbp 2 28.10 Mbp
20 5 21.80 Mbp 4 27.51 Mbp
30 8 19.67 Mbp 6 26.94 Mbp
40 11 19.03 Mbp 9 24.45 Mbp
50 15 16.32 Mbp 12 23.94 Mbp
60 19 11.44 Mbp 14 23.09 Mbp
70 27 6.85 Mbp 17 21.99 Mbp
80 42 2.59 Mbp 20 20.05 Mbp
90 0 0
100 0 0
0.878x 124 0.57 Gbp 47 0.57 Gbp
NG based on genome size 0.65 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 16 July 2021
fScaArg1.alt.cur.20210716.fasta.gz (165.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 21 2.36 Mbp 21 2.36 Mbp
20 54 1.73 Mbp 54 1.73 Mbp
30 96 1.34 Mbp 96 1.34 Mbp
40 154 0.94 Mbp 154 0.94 Mbp
50 236 0.66 Mbp 236 0.66 Mbp
60 356 443.95 Kbp 356 443.95 Kbp
70 547 255.09 Kbp 547 255.09 Kbp
80 917 121.26 Kbp 917 121.26 Kbp
90 0 0
100 0 0
0.869x 1596 0.56 Gbp 1592 0.56 Gbp
NG based on genome size 0.65 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 31 March 2020
fScaArg1.MT.20200331.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_1.7/fScaArg1.yaml (view)
species: Scatophagus_argus
specimen: fScaArg1
projects:
 - vgp
pri: s3://genomeark/species/Scatophagus_argus/fScaArg1/assembly_vgp_standard_1.7/fScaArg1.pri.20210531.fa.gz
alt: s3://genomeark/species/Scatophagus_argus/fScaArg1/assembly_vgp_standard_1.7/fScaArg1.alt.20210531.fa.gz
mito: s3://genomeark/species/Scatophagus_argus/fScaArg1/Scatophagus_argus/fScaArg1/assembly_MT_rockefeller/fScaArg1.MT.20200331.fasta.gz
pipeline:
 - falcon-kit (v1.3.0)
 - falcon-unzip (v1.2.0)
 - purge_dups (v1.2.3)
 - scaff10x (v4.2)
 - bionano_solve (Solve3.5_12162019)
 - salsa (v2.2)
 - longranger (v2.2.2)
 - pbmm2 (v1.4.0)
 - gcpp (v1.0.0-1807624)
 - bcftools (v1.12-21-ga865a16)
 - merfin (09c026d)
 - deepvariant (v1.1.0)
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.