Cyclopterus lumpus

lumpfish

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank fCycLum1: GCA_009769545.1 fCycLum1: GCA_009769515.1
ENA fCycLum1: GCA_009769545.1 fCycLum1: GCA_009769515.1
UCSC Genome Browser fCycLum1: GCA_009769545.1 fCycLum1: GCA_009769515.1

metadata.yaml (view) (edit on github)
species:
  short_name: fCycLum
  name: Cyclopterus lumpus
  taxon_id: 8103
  common_name: lumpfish
  order:
    name: Scorpaeniformes
  family:
    name: Cyclopteridae
  individuals:
    - short_name: fCycLum1
      sex:
    - short_name: fCycLum2
      biosample_id: SAMEA112789128
      sex:
  genome_size: 1000000000
  genome_size_method: null
  project: [ vgp ]
CC BY-SA 3.0 Simon Pierre Barrette (wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR fCycLum1 55.78 Gbp 55.78x 96.7 GiB
PacBio HiFi (.bam) fCycLum2 23.15 Gbp 23.15x 13.8 GiB
10x fCycLum1 61.32 Gbp 61.32x 29.3 GiB
Bionano fCycLum1 N/A 508.20x 682.5 MiB
Arima fCycLum1 89.68 Gbp 89.68x 56.3 GiB
fCycLum2 93.37 Gbp 93.37x 28.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 17 August 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fCycLum1 PacBio CLR 55.78 Gbp 55.78x 96.7 GiB
10x 61.32 Gbp 61.32x 29.3 GiB
Bionano N/A 508.20x 682.5 MiB
Arima 89.68 Gbp 89.68x 56.3 GiB
fCycLum2 PacBio HiFi (.bam) 23.15 Gbp 23.15x 13.8 GiB
Arima 93.37 Gbp 93.37x 28.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 17 August 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 11 October 2019
fCycLum1.pri.cur.20191011.fasta.gz (157.1 MiB)

Quality: 109.1 errors/Mb (QV=39.62)

Contigs Scaffolds
NG LG Len LG Len
10 8 10.80 Mbp 3 28.00 Mbp
20 20 6.41 Mbp 7 26.15 Mbp
30 38 4.35 Mbp 11 23.79 Mbp
40 74 1.96 Mbp 15 21.87 Mbp
50 146 0.91 Mbp 20 17.61 Mbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.563x 395 0.56 Gbp 48 0.57 Gbp
NG based on genome size 1.00 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 11 October 2019
fCycLum1.alt.cur.20191011.fasta.gz (136.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 47 1.31 Mbp 47 1.31 Mbp
20 150 0.75 Mbp 150 0.75 Mbp
30 334 403.95 Kbp 334 403.95 Kbp
40 747 151.08 Kbp 747 151.08 Kbp
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.481x 1866 480.97 Mbp 1866 480.97 Mbp
NG based on genome size 1.00 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 2 October 2019
fCycLum1.MT.20191002.fasta.gz (5.2 KiB)

Quality: not computed
Individual 2 Primary Assembly
Version assembly_curated from 14 September 2023
fCycLum2.pri.cur.20230914.fasta.gz (160.6 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 20 3.94 Mbp 4 27.87 Mbp
20 54 2.27 Mbp 8 26.38 Mbp
30 108 1.50 Mbp 11 24.91 Mbp
40 197 0.81 Mbp 16 22.46 Mbp
50 384 358.10 Kbp 20 20.00 Mbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.586x 1186 0.59 Gbp 232 0.59 Gbp
NG based on genome size 1.00 Gbp.
Individual 2 Alternate Assembly
Version assembly_curated from 14 September 2023
fCycLum2.alt.cur.20230914.fasta.gz (157.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 104 0.66 Mbp 104 0.66 Mbp
20 307 393.37 Kbp 307 393.37 Kbp
30 626 249.26 Kbp 626 249.26 Kbp
40 1156 144.94 Kbp 1156 144.94 Kbp
50 2191 62.53 Kbp 2191 62.53 Kbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.570x 4450 0.57 Gbp 4450 0.57 Gbp
NG based on genome size 1.00 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_cambridge from 20 August 2023
fCycLum2.MT.20230820.fasta.gz (5.6 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.