Spea bombifrons

plains spadefoot toad

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank aSpeBom1: GCA_027358695.2 aSpeBom1: GCA_027382365.2
ENA aSpeBom1: GCA_027358695.2 aSpeBom1: GCA_027382365.2
UCSC Genome Browser aSpeBom1: GCA_027358695.2 aSpeBom1: GCA_027382365.2

metadata.yaml (view) (edit on github)
species:
  name: Spea bombifrons
  individuals:
  - short_name: aSpeBom1
  short_name: aSpeBom
  taxon_id: 233779
  common_name: plains spadefoot toad
  genome_size: 1208000000
  genome_size_method: GoAT
  order:
    name: Anura
  family:
    name: Pelobatidae
  project: [ vgp ]
CC BY-NC 2.0 Andrew DuBois (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) aSpeBom1 112.12 Gbp 92.82x 277.8 GiB
PacBio HiFi (.fq) aSpeBom1 42.82 Gbp 35.45x 31.0 GiB
PacBio HiFi (.bam) aSpeBom1 43.31 Gbp 35.85x 145.0 GiB
Bionano aSpeBom1 N/A 373.08x 684.1 MiB
Arima aSpeBom1 194.61 Gbp 161.10x 98.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.21 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aSpeBom1 PacBio HiFi (subreads) 112.12 Gbp 92.82x 277.8 GiB
PacBio HiFi (.fq) 42.82 Gbp 35.45x 31.0 GiB
PacBio HiFi (.bam) 43.31 Gbp 35.85x 145.0 GiB
Bionano N/A 373.08x 684.1 MiB
Arima 194.61 Gbp 161.10x 98.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.21 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 1 April 2022
aSpeBom1.pri.cur.20220401.fasta.gz (273.5 MiB)

Quality: 0.2 errors/Mb (QV=66.30)

Contigs Scaffolds
NG LG Len LG Len
10 1 79.90 Mbp 0 165.48 Mbp
20 3 53.27 Mbp 1 143.22 Mbp
30 5 45.05 Mbp 2 123.69 Mbp
40 9 21.17 Mbp 3 114.15 Mbp
50 15 17.56 Mbp 4 109.87 Mbp
60 24 9.88 Mbp 6 47.42 Mbp
70 39 5.61 Mbp 9 41.78 Mbp
80 83 1.18 Mbp 12 29.27 Mbp
90 0 0
100 0 0
0.816x 175 0.99 Gbp 73 0.99 Gbp
NG based on genome size 1.21 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 5 February 2022
aSpeBom1.alt.cur.20220205.fasta.gz (202.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 20 4.52 Mbp 20 4.52 Mbp
20 52 2.98 Mbp 52 2.98 Mbp
30 100 2.19 Mbp 100 2.19 Mbp
40 165 1.60 Mbp 165 1.60 Mbp
50 259 1.01 Mbp 259 1.01 Mbp
60 450 331.96 Kbp 450 331.96 Kbp
70 0 0
80 0 0
90 0 0
100 0 0
0.650x 1517 0.79 Gbp 1517 0.79 Gbp
NG based on genome size 1.21 Gbp.
Assembly Metadata
aSpeBom1.yaml (view)
species: Spea_bombifrons
specimen: aSpeBom1
projects:
- vgp
primary:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/aSpeBom1.pri.asm.20220205.fasta.gz
haplotigs:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/aSpeBom1.alt.asm.20220125.fasta.gz
hic_bam:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/evaluation/pretext/s2/aSpeBom1_s2.bam
pretext:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/evaluation/pretext/s2/aSpeBom1_heatmap.pretext
kmer_spectra_img:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/evaluation/merqury/p/aSpeBom1_png/output_merqury.spectra-cn.fl.png
pipeline:
  - hifiasm (0.16.1+galaxy1)
  - purge_dups (1.2.5+galaxy3)
  - solve (3.7.0+galaxy0)
  - salsa (2.3+galaxy2)
assembly_vgp_standard_2.0/aSpeBom1.yaml (view)
species: Spea_bombifrons
specimen: aSpeBom1
projects:
- vgp
primary:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/aSpeBom1.pri.asm.20220205.fasta.gz
haplotigs:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/aSpeBom1.alt.asm.20220125.fasta.gz
hic_bam:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/evaluation/pretext/s2/aSpeBom1_s2.bam
pretext:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/evaluation/pretext/s2/aSpeBom1_heatmap.pretext
kmer_spectra_img:
    s3://genomeark/species/Spea_bombifrons/aSpeBom1/assembly_vgp_standard_2.0/evaluation/merqury/p/aSpeBom1_png/output_merqury.spectra-cn.fl.png
pipeline:
  - hifiasm (0.16.1+galaxy1)
  - purge_dups (1.2.5+galaxy3)
  - solve (3.7.0+galaxy0)
  - salsa (2.3+galaxy2)
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.