Emys orbicularis

European pond turtle

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank rEmyOrb1: GCA_028017835.1 rEmyOrb1: GCA_028017845.1
ENA rEmyOrb1: GCA_028017835.1 rEmyOrb1: GCA_028017845.1
UCSC Genome Browser rEmyOrb1: GCA_028017835.1 rEmyOrb1: GCA_028017845.1

metadata.yaml (view) (edit on github)
species:
  name: Emys orbicularis
  individuals:
  - short_name: rEmyOrb1
  short_name: rEmyOrb
  taxon_id: 82168
  common_name: European pond turtle
  genome_size: 2543000000
  genome_size_method: GoAT
  order:
    name: Testudines
  family:
    name: Emydidae
  project: [ vgp ]
CC BY 4.0 João Manuel Lemos Lima (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) rEmyOrb1 921.79 Gbp 362.48x 1.7 TiB
PacBio HiFi (.fq) rEmyOrb1 76.59 Gbp 30.12x 60.5 GiB
PacBio HiFi (.bam) rEmyOrb1 76.30 Gbp 30.00x 184.0 GiB
Bionano rEmyOrb1 N/A 229.33x 0.9 GiB
Arima rEmyOrb1 277.82 Gbp 109.25x 132.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.54 Gbp.
Last upload on 4 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rEmyOrb1 PacBio HiFi (subreads) 921.79 Gbp 362.48x 1.7 TiB
PacBio HiFi (.fq) 76.59 Gbp 30.12x 60.5 GiB
PacBio HiFi (.bam) 76.30 Gbp 30.00x 184.0 GiB
Bionano N/A 229.33x 0.9 GiB
Arima 277.82 Gbp 109.25x 132.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.54 Gbp.
Last upload on 4 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 2 September 2022
rEmyOrb1.pri.cur.20220902.fasta.gz (672.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 1 155.99 Mbp 0 373.89 Mbp
20 3 138.76 Mbp 1 300.50 Mbp
30 5 115.74 Mbp 2 217.68 Mbp
40 7 106.76 Mbp 3 158.42 Mbp
50 10 82.00 Mbp 5 137.74 Mbp
60 14 48.41 Mbp 7 114.20 Mbp
70 21 26.07 Mbp 10 81.30 Mbp
80 36 11.60 Mbp 14 34.91 Mbp
90 119 447.85 Kbp 24 18.16 Mbp
100 0 0
0.907x 254 2.31 Gbp 106 2.31 Gbp
NG based on genome size 2.54 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 2 September 2022
rEmyOrb1.alt.cur.20220902.fasta.gz (171.8 KiB)

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
0.000x 19 0.70 Mbp 19 0.70 Mbp
NG based on genome size 2.54 Gbp.
Individual 1 Haplotype 1 Assembly
Version assembly_vgp_HiC_2.0 from 1 May 2022
rEmyOrb1.HiC.hap1.20220501.fasta.gz (662.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 155.99 Mbp 1 373.28 Mbp
20 4 138.76 Mbp 2 300.50 Mbp
30 6 115.74 Mbp 3 217.68 Mbp
40 8 106.76 Mbp 4 158.16 Mbp
50 11 82.00 Mbp 6 131.90 Mbp
60 15 48.41 Mbp 8 113.37 Mbp
70 22 26.07 Mbp 11 81.37 Mbp
80 37 11.60 Mbp 16 34.22 Mbp
90 120 447.85 Kbp 32 2.75 Mbp
100 0 0
0.907x 273 2.31 Gbp 159 2.32 Gbp
NG based on genome size 2.54 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_vgp_HiC_2.0 from 1 May 2022
rEmyOrb1.HiC.hap2.20220501.fasta.gz (667.1 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 2 126.75 Mbp 1 373.37 Mbp
20 4 91.34 Mbp 2 283.82 Mbp
30 7 68.82 Mbp 3 241.59 Mbp
40 11 62.24 Mbp 4 210.33 Mbp
50 16 49.26 Mbp 6 130.99 Mbp
60 21 37.54 Mbp 8 107.85 Mbp
70 29 25.86 Mbp 11 81.17 Mbp
80 43 11.54 Mbp 15 37.56 Mbp
90 114 0.84 Mbp 32 2.38 Mbp
100 0 0
0.913x 267 2.32 Gbp 137 2.33 Gbp
NG based on genome size 2.54 Gbp.
Assembly Metadata
assembly_vgp_HiC_2.0/rEmyOrb1.yaml (view)
species: Emys orbicularis
specimen: rEmyOrb1
projects: 
  - vgp
hap1: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/assembly_vgp_HiC_2.0/rEmyOrb1.HiC.hap1.20220501.fasta.gz
hap2: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/assembly_vgp_HiC_2.0/rEmyOrb1.HiC.hap2.20220501.fasta.gz
hap1_hic_bam: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/rEmyOrb1_hap1__s2.bam
hap2_hic_bam: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/rEmyOrb1_hap2__s2.bam
hap1_pretext: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/assembly_vgp_HiC_2.0/evaluation/hap1/rEmyOrb1_hap1__s2_heatmap.pretext
hap2_pretext: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/assembly_vgp_HiC_2.0/evaluation/hap2/rEmyOrb1_hap2__s2_heatmap.pretext
kmer_spectra_img: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/assembly_vgp_HiC_2.0/evaluation/rEmyOrb1_png/
pacbio_read_dir: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/genomic_data/arima/
bionano_cmap_dir: s3://genomeark/species/Emys_orbicularis/rEmyOrb1/genomic_data/bionano/
pipeline: 
  - hifiasm (0.16.1+galaxy2)
  - solve (3.7.0+galaxy0)
  - salsa (2.3+galaxy2)
assembled_by_group: University of Florence
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.