Erythrolamprus reginae

royal ground snake

Included in the VGP.

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


metadata.yaml (view) (edit on github)
species:
  name: Erythrolamprus reginae
  individuals:
  - short_name: rEryReg1
  short_name: rEryReg
  taxon_id: 121349
  common_name: royal ground snake
  genome_size: 1966000000
  genome_size_method: GoAT
  order:
    name: Squamata
  family:
    name: Dipsadidae
  project: [ vgp ]
CC BY-NC 4.0 Omar Rojas-Padilla (iNaturalist)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rEryReg1 808.90 Gbp 411.44x 1.4 TiB
PacBio HiFi (.fq) rEryReg1 67.76 Gbp 34.47x 55.2 GiB
PacBio HiFi (.bam) rEryReg1 58.95 Gbp 29.99x 158.8 GiB
Bionano rEryReg1 N/A 178.82x 589.0 MiB
Arima rEryReg1 200.15 Gbp 101.81x 98.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.97 Gbp.
Last upload on 4 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rEryReg1 PacBio HiFi (subreads) 808.90 Gbp 411.44x 1.4 TiB
PacBio HiFi (.fq) 67.76 Gbp 34.47x 55.2 GiB
PacBio HiFi (.bam) 58.95 Gbp 29.99x 158.8 GiB
Bionano N/A 178.82x 589.0 MiB
Arima 200.15 Gbp 101.81x 98.7 GiB
Bases and Coverage are approximate.
Coverage based on genome size 1.97 Gbp.
Last upload on 4 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 5 January 2023
rEryReg1.pri.cur.20230105.fasta.gz (548.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 15 10.44 Mbp 0 426.56 Mbp
20 38 7.41 Mbp 0 426.56 Mbp
30 70 5.13 Mbp 1 355.37 Mbp
40 115 3.89 Mbp 2 259.12 Mbp
50 172 3.01 Mbp 2 259.12 Mbp
60 247 2.28 Mbp 3 152.91 Mbp
70 346 1.68 Mbp 5 119.10 Mbp
80 498 1.02 Mbp 7 87.32 Mbp
90 774 486.12 Kbp 10 50.30 Mbp
100 0 0
0.979x 1712 1.92 Gbp 325 1.92 Gbp
NG based on genome size 1.97 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 5 January 2023
rEryReg1.alt.cur.20230105.fasta.gz (11.1 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
0.020x 80 39.45 Mbp 76 39.45 Mbp
NG based on genome size 1.97 Gbp.
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 8 March 2023
rEryReg1.HiC.hap1.20230308.fasta.gz (533.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 14 11.32 Mbp 14 11.32 Mbp
20 34 8.66 Mbp 34 8.66 Mbp
30 59 6.97 Mbp 59 6.97 Mbp
40 90 5.58 Mbp 90 5.58 Mbp
50 130 4.46 Mbp 130 4.46 Mbp
60 179 3.59 Mbp 179 3.59 Mbp
70 241 2.81 Mbp 241 2.81 Mbp
80 328 1.80 Mbp 328 1.80 Mbp
90 469 1.07 Mbp 469 1.07 Mbp
100 754 398.44 Kbp 754 398.44 Kbp
1.037x 1136 2.04 Gbp 1136 2.04 Gbp
NG based on genome size 1.97 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 23 June 2023
rEryReg1.hap2.cur.20230623.fasta.gz (548.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 16 10.44 Mbp 1 426.56 Mbp
20 39 7.41 Mbp 1 426.56 Mbp
30 71 5.13 Mbp 2 355.37 Mbp
40 116 3.89 Mbp 3 259.12 Mbp
50 173 3.01 Mbp 3 259.12 Mbp
60 248 2.28 Mbp 4 152.91 Mbp
70 347 1.68 Mbp 6 119.10 Mbp
80 499 1.02 Mbp 8 87.32 Mbp
90 775 486.12 Kbp 11 50.30 Mbp
100 0 0
0.979x 1712 1.92 Gbp 325 1.92 Gbp
NG based on genome size 1.97 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/rEryReg1_hap2.yaml (view)
species: Erythrolamprus reginae
specimen: rEryReg1
projects: 
  - vgp
hap2: s3://genomeark/species/Erythrolamprus_reginae/rEryReg1/assembly_vgp_HiC_2.0/rEryReg1.HiC.hap2.20220929.fasta.gz
pretext_hap2: s3://genomeark/species/Erythrolamprus_reginae/rEryReg1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rEryReg1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Erythrolamprus_reginae/rEryReg1/assembly_vgp_HiC_2.0/evaluation/rEryReg1_png/
pacbio_read_dir: s3://genomeark/species/Erythrolamprus_reginae/rEryReg1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Erythrolamprus_reginae/rEryReg1/genomic_data/arima/
pipeline:
  - hifiasm (0.16.1+galaxy3)
  - yahs (1.2a+galaxy1)
assembled_by_group: Rockefeller
notes: GenomeScope exploration of the raw data indicates this specimen is likely to be triploid (model fits well at p=3); smudgeplot also results in "proposed triploid", with a strong AAB signal on the smudgeplot. Hifiasm-HiC assembly resulted in hap1 and hap2 assemblies, with hap1 looking to have two copies of the genome based on QC metrics, while hap2 has one un-duplicated copy of the genome. This is supported by largely unduplicated BUSCO results (3189 complete genes out of 3354, with 3099 single copy and 90 dupes), a largely 1-copy kmer-cn spectrum, and the length of the assembly being near to the expected genome size based on the triploid genomescope model. This hap2 was scaffolded with HiC data using YAHS, and is what we are submitting for curation. 
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.