Bombina bombina

European fire-bellied toad

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank aBomBom1: GCA_027579735.1 aBomBom1: GCA_027579415.1
ENA aBomBom1: GCA_027579735.1 aBomBom1: GCA_027579415.1
UCSC Genome Browser aBomBom1: GCA_027579735.1 aBomBom1: GCA_027579415.1

metadata.yaml (view) (edit on github)
species:
  short_name: aBomBom
  name: Bombina bombina
  taxon_id: 8345
  common_name: European fire-bellied toad
  order:
    name: Anura
  family:
    name: Bombinatoridae
  individuals:
    - short_name: aBomBom1
  project: [ vgp ]
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR aBomBom1 929.36 Gbp 92.75x 1.6 TiB
PacBio CLR (.fq) aBomBom1 163.69 Gbp 16.34x 288.3 GiB
10x aBomBom1 703.90 Gbp 70.25x 326.9 GiB
Bionano aBomBom1 N/A 364.07x 8.7 GiB
Arima aBomBom1 1466.58 Gbp 146.37x 684.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 10.02 Gbp.
Last upload on 27 June 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aBomBom1 PacBio CLR 929.36 Gbp 92.75x 1.6 TiB
PacBio CLR (.fq) 163.69 Gbp 16.34x 288.3 GiB
10x 703.90 Gbp 70.25x 326.9 GiB
Bionano N/A 364.07x 8.7 GiB
Arima 1466.58 Gbp 146.37x 684.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 10.02 Gbp.
Last upload on 27 June 2023.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 8 April 2022
aBomBom1.pri.cur.20220408.fasta.gz (2.7 GiB)

Quality: 125.3 errors/Mb (QV=39.02)

Contigs Scaffolds
NG LG Len LG Len
10 71 10.74 Mbp 0 1.60 Gbp
20 181 7.65 Mbp 1 1.45 Gbp
30 325 5.99 Mbp 1 1.45 Gbp
40 508 4.79 Mbp 2 1.30 Gbp
50 739 3.71 Mbp 3 1.24 Gbp
60 1044 2.79 Mbp 4 1.17 Gbp
70 1460 2.01 Mbp 5 1.16 Gbp
80 2067 1.29 Mbp 6 0.64 Gbp
90 3184 0.58 Mbp 8 291.27 Mbp
100 9475 305 bp 2466 711 bp
1.000x 9476 9.82 Gbp 2467 10.02 Gbp
NG based on genome size 10.02 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 8 April 2022
aBomBom1.alt.cur.20220408.fasta.gz (1.5 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 761 0.54 Mbp 733 0.54 Mbp
20 1937 388.12 Kbp 1898 392.10 Kbp
30 3523 293.48 Kbp 3475 295.29 Kbp
40 5614 225.43 Kbp 5557 226.40 Kbp
50 8305 176.33 Kbp 8242 176.91 Kbp
60 11711 141.00 Kbp 11643 141.30 Kbp
70 15917 115.39 Kbp 15846 115.53 Kbp
80 21052 93.63 Kbp 20980 93.72 Kbp
90 27604 70.02 Kbp 27530 70.11 Kbp
100 39464 202 bp 39373 202 bp
1.000x 39465 5.35 Gbp 39374 5.35 Gbp
NG based on genome size 10.02 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 24 November 2022
aBomBom1.MT.20221124.fasta.gz (5.1 KiB)

Quality: not computed
Assembly Metadata
aBomBom1.yaml (view)
species: Bombina bombina
specimen: aBomBom1
projects:
  - vgp
primary: s3://genomeark/species/Bombina_bombina/aBomBom1/assembly_vgp_standard_1.6/aBomBom1.pri.20210531.fasta.gz
haplotigs: s3://genomeark/species/Bombina_bombina/aBomBom1/assembly_vgp_standard_1.6/aBomBom1.alt.20210531.fasta.gz
pacbio_read_dir: s3://genomearkspecies/Bombina_bombina/aBomBom1/genomic_data/pacbio/
pacbio_read_type: clr
pipeline:
  - Falcon-kit (1.8.1)
  - falcon_unzip (1.3.7)
  - purge_dups (1.2.3)
  - scaff10x (4.2a)
  - bionano_solve (Solve3.6.1_11162020)
  - salsa2  (2.2)
  - longranger (2.2.2)
  - gcpp (2.0.2)
  - freebayes (1.3.2)
assembled_by_group: Dresden
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.