Malaclemys terrapin

diamondback terrapin

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank rMalTer1: GCA_027887155.1 rMalTer1: GCA_027887205.1
ENA rMalTer1: GCA_027887155.1 rMalTer1: GCA_027887205.1
UCSC Genome Browser rMalTer1: GCA_027887155.1 rMalTer1: GCA_027887205.1

metadata.yaml (view) (edit on github)
species:
  name: Malaclemys terrapin
  individuals:
  - short_name: rMalTer1
  short_name: rMalTer
  taxon_id: 8485
  common_name: diamondback terrapin
  genome_size: 2670000000
  genome_size_method: GoAT
  order:
    name: Testudines
  family:
    name: Emydidae
  project: [ vgp ]
CC BY 2.5 J.D. Wilson (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) rMalTer1 80.79 Gbp 30.26x 63.0 GiB
Bionano rMalTer1 N/A 833.79x 3.6 GiB
Arima rMalTer1 184.19 Gbp 68.98x 94.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.67 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rMalTer1 PacBio HiFi (.fq) 80.79 Gbp 30.26x 63.0 GiB
Bionano N/A 833.79x 3.6 GiB
Arima 184.19 Gbp 68.98x 94.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.67 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 8 July 2022
rMalTer1.hap1.cur.20220708.fasta.gz (646.5 MiB)

Quality: 0.2 errors/Mb (QV=67.68)

Contigs Scaffolds
NG LG Len LG Len
10 1 133.80 Mbp 0 356.04 Mbp
20 4 108.60 Mbp 1 287.94 Mbp
30 6 94.60 Mbp 2 209.48 Mbp
40 10 75.59 Mbp 4 144.57 Mbp
50 14 52.97 Mbp 6 128.56 Mbp
60 20 37.20 Mbp 8 106.34 Mbp
70 29 22.09 Mbp 12 46.69 Mbp
80 59 3.22 Mbp 21 20.00 Mbp
90 0 0
100 0 0
0.828x 217 2.21 Gbp 76 2.21 Gbp
NG based on genome size 2.67 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 8 July 2022
rMalTer1.hap2.cur.20220708.fasta.gz (647.4 MiB)

Quality: 0.2 errors/Mb (QV=67.80)

Contigs Scaffolds
NG LG Len LG Len
10 1 182.37 Mbp 0 356.04 Mbp
20 3 134.96 Mbp 1 287.23 Mbp
30 5 120.02 Mbp 2 209.33 Mbp
40 7 97.70 Mbp 4 143.97 Mbp
50 10 78.53 Mbp 6 128.41 Mbp
60 15 44.68 Mbp 8 105.66 Mbp
70 22 21.36 Mbp 12 48.33 Mbp
80 47 3.75 Mbp 21 20.68 Mbp
90 0 0
100 0 0
0.829x 186 2.21 Gbp 59 2.21 Gbp
NG based on genome size 2.67 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/rMalTer1.yaml (view)
species: Malaclemys terrapin
specimen: rMalTer1
projects:
  - vgp
hap1: s3://genomeark/species/Malaclemys_terrapin/rMalTer1/assembly_vgp_HiC_2.0/rMalTer1.HiC.hap1.20220601.fasta.gz
hap2: s3://genomeark/species/Malaclemys_terrapin/rMalTer1/assembly_vgp_HiC_2.0/rMalTer1.HiC.hap2.20220601.fasta.gz
hap1_hic_bam: s3://genomeark/species/Malaclemys_terrapin/rMalTer1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rMalTer1_hap1__s2.bam
hap2_hic_bam: s3://genomeark/species/Malaclemys_terrapin/rMalTer1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rMalTer1_hap2__s2.bam
hap1_pretext: s3://genomeark/species/Malaclemys_terrapin/rMalTer1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rMalTer1_hap1__s2_heatmap.pretext
hap2_pretext: s3://genomeark/species/Malaclemys_terrapin/rMalTer1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rMalTer1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Malaclemys_terrapin/rMalTer1/assembly_vgp_HiC_2.0/evaluation/merqury/rMalTer1_png/
pipeline:
  - hifiasm (0.16.1+galaxy2)
  - solve (3.7)
  - 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.