Grus americana

Whooping crane

Included in the VGP.

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


Resource Maternal Assembly Paternal Assembly
GenBank bGruAme1: GCA_028858705.1 bGruAme1: GCA_028858595.1
ENA bGruAme1: GCA_028858705.1 bGruAme1: GCA_028858595.1
UCSC Genome Browser bGruAme1: GCA_028858705.1 bGruAme1: GCA_028858595.1

metadata.yaml (view) (edit on github)
species:
  short_name: bGruAme
  name: Grus americana
  taxon_id: 9117
  common_name: Whooping crane
  order:
    name: Gruiformes
  family:
    name: Gruidae
  individuals:
    - short_name: bGruAme1
  genome_size: 1000000000
  genome_size_method:
  project: [ vgp ]
CC BY 2.0 U.S. Fish and Wildlife Services (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR bGruAme1 232.67 Gbp 232.67x 419.4 GiB
10x bGruAme1 111.13 Gbp 111.13x 55.1 GiB
Bionano bGruAme1 N/A 417.39x 635.8 MiB
Arima bGruAme1 93.77 Gbp 93.77x 60.2 GiB
Illumina bGruAme2 87.69 Gbp 87.69x 41.9 GiB
bGruAme3 87.90 Gbp 87.90x 41.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 19 April 2021.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
bGruAme1 PacBio CLR 232.67 Gbp 232.67x 419.4 GiB
10x 111.13 Gbp 111.13x 55.1 GiB
Bionano N/A 417.39x 635.8 MiB
Arima 93.77 Gbp 93.77x 60.2 GiB
bGruAme2 Illumina 87.69 Gbp 87.69x 41.9 GiB
bGruAme3 Illumina 87.90 Gbp 87.90x 41.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.00 Gbp.
Last upload on 19 April 2021.
Assemblies
Individual 1 Maternal Assembly
Version assembly_curated from 16 February 2023
bGruAme1.mat.cur.20230216.fasta.gz (358.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 104.20 Mbp 0 219.87 Mbp
20 2 71.64 Mbp 1 169.58 Mbp
30 4 55.79 Mbp 1 169.58 Mbp
40 6 49.58 Mbp 2 126.35 Mbp
50 10 28.32 Mbp 4 82.90 Mbp
60 15 21.62 Mbp 5 71.43 Mbp
70 21 16.76 Mbp 8 36.57 Mbp
80 30 9.75 Mbp 13 23.24 Mbp
90 51 2.67 Mbp 21 9.56 Mbp
100 1096 1.63 Kbp 835 1.63 Kbp
1.000x 1097 1.25 Gbp 836 1.25 Gbp
NG based on genome size 1.00 Gbp.
Individual 1 Paternal Assembly
Version assembly_curated from 16 February 2023
bGruAme1.pat.cur.20230216.fasta.gz (347.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 17.21 Mbp 0 218.30 Mbp
20 12 14.03 Mbp 1 167.27 Mbp
30 22 11.01 Mbp 1 167.27 Mbp
40 33 9.48 Mbp 2 125.20 Mbp
50 47 7.12 Mbp 3 86.83 Mbp
60 67 5.41 Mbp 5 70.63 Mbp
70 94 3.64 Mbp 7 41.61 Mbp
80 136 2.31 Mbp 12 23.92 Mbp
90 216 0.96 Mbp 18 14.19 Mbp
100 853 892 bp 267 892 bp
1.000x 854 1.19 Gbp 268 1.19 Gbp
NG based on genome size 1.00 Gbp.
Assembly Metadata
assembly_vgp_trio_1.7/bGruAme1_mat.yaml (view)
species: Grus Americana
specimen: bGruAme1
projects:
  - vgp
mat: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/bGruAme1.mat.asm.20220516.fasta.gz
mat_hic_bam: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/qc/pretext/mat/bGruAme1.mat.asm.20220516.bam 
mat_pretext: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/qc/pretext/mat/bGruAme1.mat.asm.20220516.pretext
kmer_spectra_img: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/qc/merqury/longranger_freebayes_2/fb1_t3.spectra-asm.fl.png
pipeline:
 
- TrioCanu v. 2.1 
- purge_dups v. 1.0.0; 
- Scaff 10x v. 4.1.0; 
- bionano Solve v. 3.6.1_11162020 
- Salsa2 HiC v. 2.2; 
- gcpp (Arrow polishing) v. 2.0.2-2.0.2
- merfin v. 1.0
- Freebayes v. 1.3.1; 
 
assembly_vgp_trio_1.7/bGruAme1_pat.yaml (view)
species: Grus Americana
specimen: bGruAme1
projects:
  - vgp
pat: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/bGruAme1.pat.asm.20220516.fasta.gz
pat_hic_bam: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/qc/pretext/pat/bGruAme1.pat.asm.20220516.bam 
pat_pretext: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/qc/pretext/pat/bGruAme1.pat.asm.20220516.pretext
kmer_spectra_img: s3://genomeark/species/Grus_americana/bGruAme1/assembly_vgp_trio_1.7/qc/merqury/longranger_freebayes_2/fb1_t3.spectra-asm.fl.png
pipeline:
 
- TrioCanu v. 2.1 
- purge_dups v. 1.0.0; 
- Scaff 10x v. 4.1.0; 
- bionano Solve v. 3.6.1_11162020 
- Salsa2 HiC v. 2.2; 
- gcpp (Arrow polishing) v. 2.0.2-2.0.2
- merfin v. 1.0
- Freebayes v. 1.3.1; 
 
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.