Diceros bicornis

black rhinoceros

Included in the VGP.

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


Resource Maternal Assembly Paternal Assembly
GenBank mDicBic1: GCA_020826845.1 mDicBic1: GCA_020826835.1
ENA mDicBic1: GCA_020826845.1 mDicBic1: GCA_020826835.1
UCSC Genome Browser mDicBic1: GCA_020826845.1 mDicBic1: GCA_020826835.1

metadata.yaml (view) (edit on github)
species:
  short_name: mDicBic
  name: Diceros bicornis
  taxon_id: 9805
  common_name: black rhinoceros
  order:
    name: Perissodactyla
  family:
    name: Rhinocerotidae
  individuals:
    - short_name: mDicBic1
      provider: Budhan Pukazhenthi, Klaus Koepfli
      sex: female
      mother: mDicBic2
      father: mDicBic3
      subspecies:
        name: Diceros bicornis bicornis
        common_name: southern black rhinoceros
        taxon_id: 1081385
    - short_name: mDicBic2
      provider: Budhan Pukazhenthi, Klaus Koepfli
      sex: female
      subspecies:
        name: Diceros bicornis bicornis
        common_name: southern black rhinoceros
        taxon_id: 1081385
    - short_name: mDicBic3
      provider: Budhan Pukazhenthi, Klaus Koepfli
      sex: male
      subspecies:
        name: Diceros bicornis bicornis
        common_name: southern black rhinoceros
        taxon_id: 1081385
  genome_size: 3000000000
  genome_size_method:
  project: [ vgp ]
CC BY-NC-SA 2.0 Arno Meintjes (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mDicBic1 1687.25 Gbp 562.42x 3.0 TiB
PacBio HiFi (.bam) mDicBic1 91.93 Gbp 30.64x 76.9 GiB
Bionano mDicBic1 N/A 791.92x 4.6 GiB
Arima mDicBic1 218.61 Gbp 72.87x 148.4 GiB
Illumina mDicBic2 286.35 Gbp 95.45x 133.3 GiB
mDicBic3 136.49 Gbp 45.50x 63.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.00 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mDicBic1 PacBio HiFi (subreads) 1687.25 Gbp 562.42x 3.0 TiB
PacBio HiFi (.bam) 91.93 Gbp 30.64x 76.9 GiB
Bionano N/A 791.92x 4.6 GiB
Arima 218.61 Gbp 72.87x 148.4 GiB
mDicBic2 Illumina 286.35 Gbp 95.45x 133.3 GiB
mDicBic3 Illumina 136.49 Gbp 45.50x 63.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.00 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Maternal Assembly
Version assembly_curated from 16 July 2021
mDicBic1.mat.cur.20210716.fasta.gz (832.1 MiB)

Quality: 2.8 errors/Mb (QV=55.48)

Contigs Scaffolds
NG LG Len LG Len
10 3 72.36 Mbp 2 103.33 Mbp
20 8 57.68 Mbp 5 95.94 Mbp
30 13 52.99 Mbp 8 87.87 Mbp
40 20 37.17 Mbp 12 78.38 Mbp
50 30 28.47 Mbp 16 65.03 Mbp
60 42 21.09 Mbp 21 59.65 Mbp
70 58 16.41 Mbp 27 46.42 Mbp
80 81 8.35 Mbp 34 37.10 Mbp
90 169 1.59 Mbp 53 3.87 Mbp
100 1155 38.79 Kbp 907 42.32 Kbp
1.001x 1290 3.00 Gbp 1075 3.01 Gbp
NG based on genome size 3.00 Gbp.
Individual 1 Paternal Assembly
Version assembly_curated from 16 July 2021
mDicBic1.pat.decon.20210716.fasta.gz (845.3 MiB)

Quality: 3.0 errors/Mb (QV=55.17)

Contigs Scaffolds
NG LG Len LG Len
10 3 78.03 Mbp 2 96.73 Mbp
20 7 64.02 Mbp 5 86.64 Mbp
30 13 42.80 Mbp 9 78.03 Mbp
40 21 33.29 Mbp 13 66.77 Mbp
50 31 28.78 Mbp 18 59.08 Mbp
60 43 21.06 Mbp 24 48.17 Mbp
70 59 14.84 Mbp 31 35.88 Mbp
80 88 8.30 Mbp 40 25.47 Mbp
90 162 1.97 Mbp 68 4.05 Mbp
100 622 146.66 Kbp 445 165.21 Kbp
1.015x 1377 3.04 Gbp 1199 3.04 Gbp
NG based on genome size 3.00 Gbp.
Assembly Metadata
assembly_vgp_hifi/mDicBic1.yaml (view)
species: Diceros_bicornis
specimen: mDicBic1
projects:
  - vgp
mat: s3://genomeark/species/Diceros_bicornis/mDicBic1/assembly_vgp_hifi/mDicBic1.mat.asm.20210507.fasta.gz
pat: s3://genomeark/species/Diceros_bicornis/mDicBic1/assembly_vgp_hifi/mDicBic1.pat.asm.20210507.fasta.gz
mat_hic_bam: s3://genomeark/species/Diceros_bicornis/mDicBic1/assembly_vgp_hifi/evaluation/pretext/mat_s2/mDicBic1_mat_s2.bam
pat_hic_bam: s3://genomeark/species/Diceros_bicornis/mDicBic1/assembly_vgp_hifi/evaluation/pretext/pat_s2/mDicBic1_pat_s2.bam
pipeline:
  - hifiasm (0.15.1-r329)
  - bionano_solve (Solve3.6.1_11162020)
  - salsa (v2.2)
mDicBic1_metadata.yml (view)
samples:
- Sample Source: Smithsonian Conservation Biology Institute
  VGP_Id: mDicBic1
  birth_date: ''
  collected_by: Budhan Pukazhenthi
  collection_date: 03/20/2016
  common_name: black rhinoceros
  description: 'For VGP sequencing - trio binning. This is the DAUGHTER.; subspecies:
    Diceros bicornis bicornis'
  dev_stage: juvenile
  geo_loc_name: USA
  individual_id: ''
  lat_lon: ''
  scientific_name: Diceros bicornis
  sex: female
  store_cond: -80C
  taxon_Id: '9805'
  tissue: Blood
  treatment: Flash Frozen
  tube_id: mDicBic1.BL4,mDicBic1.BL2,mDicBic1.BL1
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.