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 (subreads) rMalTer1 300.97 Gbp 112.72x 704.1 GiB
PacBio HiFi (.fq) rMalTer1 80.79 Gbp 30.26x 63.0 GiB
PacBio HiFi (.bam) rMalTer1 73.20 Gbp 27.42x 253.4 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 28 April 2026.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rMalTer1 PacBio HiFi (subreads) 300.97 Gbp 112.72x 704.1 GiB
PacBio HiFi (.fq) 80.79 Gbp 30.26x 63.0 GiB
PacBio HiFi (.bam) 73.20 Gbp 27.42x 253.4 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 28 April 2026.
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.