Cinclus cinclus

white-throated dipper

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  short_name: bCinCin
  name: Cinclus cinclus
  taxon_id: 127875
  common_name: white-throated dipper
  order:
    name: Passeriformes
  family:
    name: Cinclidae
  individuals:
    - short_name: bCinCin1
      biosample_id: SAMEA9679959
      sex:
    - short_name: bCinCin2
      biosample_id: SAMEA9679961
      sex: male
  genome_size:
  genome_size_method:
  project: [ vgp ]
CC BY 2.0, Dirk-Jan van Roest (wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.bam) bCinCin1 50.26 Gbp 42.92x 31.8 GiB
Arima bCinCin2 94.78 Gbp 80.95x 45.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.17 Gbp.
Last upload on 19 June 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bCinCin1 PacBio HiFi (.bam) 50.26 Gbp 42.92x 31.8 GiB
bCinCin2 Arima 94.78 Gbp 80.95x 45.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.17 Gbp.
Last upload on 19 June 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 9 November 2023
bCinCin1.pri.cur.20231109.fasta.gz (317.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 13 8.36 Mbp 1 152.36 Mbp
20 29 6.72 Mbp 2 117.95 Mbp
30 48 5.48 Mbp 3 117.73 Mbp
40 73 4.26 Mbp 4 85.38 Mbp
50 103 3.56 Mbp 6 74.36 Mbp
60 141 2.73 Mbp 8 38.63 Mbp
70 189 2.11 Mbp 12 25.57 Mbp
80 257 1.39 Mbp 17 17.50 Mbp
90 364 0.83 Mbp 27 8.30 Mbp
100 936 1.00 Kbp 278 1.00 Kbp
1.000x 936 1.17 Gbp 278 1.17 Gbp
NG based on genome size 1.17 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 9 November 2023
bCinCin1.alt.cur.20231109.fasta.gz (291.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 69 1.16 Mbp 69 1.16 Mbp
20 176 0.84 Mbp 176 0.84 Mbp
30 321 0.66 Mbp 321 0.66 Mbp
40 502 0.52 Mbp 502 0.52 Mbp
50 725 431.28 Kbp 725 431.28 Kbp
60 997 345.24 Kbp 997 345.24 Kbp
70 1345 266.97 Kbp 1345 266.97 Kbp
80 1812 187.93 Kbp 1812 187.93 Kbp
90 2547 107.28 Kbp 2547 107.28 Kbp
100 4724 7.08 Kbp 4724 7.08 Kbp
1.000x 4724 1.06 Gbp 4724 1.06 Gbp
NG based on genome size 1.17 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_cambridge from 9 May 2023
bCinCin1.MT.20230509.fasta.gz (5.4 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.