Pelobates fuscus

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Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.bam) aPelFus1 91.66 Gbp N/A 292.7 GiB
Arima aPelFus1 172.58 Gbp N/A 80.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 April 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aPelFus1 PacBio HiFi (.bam) 91.66 Gbp N/A 292.7 GiB
Arima 172.58 Gbp N/A 80.6 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 5 April 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 23 June 2023
aPelFus1.hap1.decon.20230623.fasta.gz (1.0 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 16 16.35 Mbp 1 493.56 Mbp
20 41 12.72 Mbp 2 445.67 Mbp
30 73 10.01 Mbp 3 421.46 Mbp
40 113 8.16 Mbp 4 385.98 Mbp
50 161 6.50 Mbp 5 381.96 Mbp
60 225 4.92 Mbp 6 310.34 Mbp
70 309 3.69 Mbp 7 183.86 Mbp
80 423 2.69 Mbp 9 170.33 Mbp
90 593 1.50 Mbp 11 143.22 Mbp
100 1382 1.00 Kbp 270 1.00 Kbp
1.000x 1382 3.57 Gbp 270 3.57 Gbp
NG based on genome size .
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 23 June 2023
aPelFus1.hap2.decon.20230623.fasta.gz (1.0 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 17 16.09 Mbp 1 496.21 Mbp
20 42 12.31 Mbp 2 435.41 Mbp
30 75 9.82 Mbp 3 426.39 Mbp
40 117 7.50 Mbp 4 385.95 Mbp
50 170 5.89 Mbp 5 384.56 Mbp
60 238 4.70 Mbp 6 310.36 Mbp
70 324 3.67 Mbp 7 183.81 Mbp
80 438 2.67 Mbp 9 173.50 Mbp
90 613 1.54 Mbp 11 142.89 Mbp
100 1213 1.00 Kbp 109 1.00 Kbp
1.000x 1213 3.58 Gbp 109 3.58 Gbp
NG based on genome size .
Individual 1 Mitochondrial Assembly
Version assembly_vgp_HiC_2.0 from 8 March 2023
aPelFus1.mito.20230308.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/aPelFus1.yaml (view)
species: Pelobates fuscus
specimen: aPelFus1
projects:
  - VGP
release_to: S3
data_location: S3
hap1: s3://genomeark/species/Pelobates_fuscus/aPelFus1/assembly_vgp_HiC_2.0/aPelFus1.HiC.hap1.20230308.fasta.gz
hap2: s3://genomeark/species/Pelobates_fuscus/aPelFus1/assembly_vgp_HiC_2.0/aPelFus1.HiC.hap2.20230308.fasta.gz
primary: s3://genomeark/species/Pelobates_fuscus/aPelFus1/assembly_vgp_HiC_2.0/aPelFus1.HiC.pctg.20230308.fasta.gz
mito: s3://genomeark/species/Pelobates_fuscus/aPelFus1/assembly_vgp_HiC_2.0/aPelFus1.mito.20230308.fasta.gz
pacbio_read_dir: s3://genomeark/species/Pelobates_fuscus/aPelFus1/genomic_data/pacbio/ 
hic_read_dir: s3://genomeark/species/Pelobates_fuscus/aPelFus1/genomic_data/arima/
pipeline:
  - deepconsensus (1.1)
  - hifiasm (0.18.7-r519)
  - purge_dups (1.2.5)
  - yahs (1.2a.2)
  - deepVariant polishing (1.4)
  - MitoHiFi (3.0.0)
assembled_by_group: MPI-CBG
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.