Podarcis raffonei

Aeolian wall lizard

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank rPodRaf1: GCA_027172205.1 rPodRaf1: GCA_027172095.1
ENA rPodRaf1: GCA_027172205.1 rPodRaf1: GCA_027172095.1
UCSC Genome Browser rPodRaf1: GCA_027172205.1 rPodRaf1: GCA_027172095.1

metadata.yaml (view) (edit on github)
species:
  name: Podarcis raffonei
  individuals:
  - short_name: rPodRaf1
  short_name: rPodRaf
  taxon_id: 65483
  common_name: Aeolian wall lizard
  genome_size: 1949000000
  genome_size_method: GoAT
  order:
    name: Squamata
  family:
    name: Lacertidae
  project: [ vgp ]
CC BY-SA 3.0 Federico Muciaccia (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rPodRaf1 773.36 Gbp 396.80x 1.4 TiB
PacBio HiFi (.fq) rPodRaf1 60.52 Gbp 31.05x 47.7 GiB
PacBio HiFi (.bam) rPodRaf1 34.44 Gbp 17.67x 27.8 GiB
Bionano rPodRaf1 N/A 305.50x 1.1 GiB
Arima rPodRaf1 440.21 Gbp 225.86x 205.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.95 Gbp.
Last upload on 13 May 2024.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rPodRaf1 PacBio HiFi (subreads) 773.36 Gbp 396.80x 1.4 TiB
PacBio HiFi (.fq) 60.52 Gbp 31.05x 47.7 GiB
PacBio HiFi (.bam) 34.44 Gbp 17.67x 27.8 GiB
Bionano N/A 305.50x 1.1 GiB
Arima 440.21 Gbp 225.86x 205.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.95 Gbp.
Last upload on 13 May 2024.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 26 January 2022
rPodRaf1.pri.cur.20220126.fasta.gz (435.7 MiB)

Quality: 0.6 errors/Mb (QV=62.55)

Contigs Scaffolds
NG LG Len LG Len
10 1 104.57 Mbp 1 127.26 Mbp
20 3 93.60 Mbp 2 124.66 Mbp
30 6 67.80 Mbp 4 102.32 Mbp
40 9 61.44 Mbp 6 93.62 Mbp
50 12 55.22 Mbp 9 79.25 Mbp
60 16 43.50 Mbp 11 61.44 Mbp
70 23 17.46 Mbp 15 45.10 Mbp
80 0 0
90 0 0
100 0 0
0.776x 57 1.51 Gbp 27 1.51 Gbp
NG based on genome size 1.95 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 26 January 2022
rPodRaf1.alt.cur.20220126.fasta.gz (52.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 0 0
20 0 0
30 0 0
40 0 0
50 0 0
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.093x 4814 182.03 Mbp 4811 182.03 Mbp
NG based on genome size 1.95 Gbp.
Assembly Metadata
assembly_vgp_standard_2.0/rPodRaf1.yaml (view)
species: Podarcis raffonei
specimen: rPodRaf1
projects:
  - vgp
primary: s3://genomeark/species/Podarcis_raffonei/rPodRaf1/assembly_vgp_standard_2.0/rPodRaf1.pri.asm.20211118.fasta.gz
haplotigs: s3://genomeark/species/Podarcis_raffonei/rPodRaf1/assembly_vgp_standard_2.0/rPodRaf1.alt.asm.20211118.fasta.gz
hic_bam: s3://genomeark/species/Podarcis_raffonei/rPodRaf1/assembly_vgp_standard_2.0/evaluation/pretext/s2/rPodRaf1.bam
pretext: s3://genomeark/species/Podarcis_raffonei/rPodRaf1/assembly_vgp_standard_2.0/evaluation/pretext/s2/rPodRaf1.pretext
kmer_spectra_img: s3://genomeark/species/Podarcis_raffonei/rPodRaf1/assembly_vgp_standard_2.0/evaluation/merqury/p1q2_hifi/p1q2.hifi.spectra-cn.fl.png
pipeline:
  - hifiasm (0.16.1-r375)
  - purge_dups (1.2.5)
  - bionano_solve (3.6.1)
  - salsa (2.3)
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.