Gopherus flavomarginatus

Mexican gopher tortoise

Included in the VGP.

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


Resource Maternal Assembly Paternal Assembly
GenBank rGopFla2: GCA_025201925.1 rGopFla2: GCA_025201965.1
ENA rGopFla2: GCA_025201925.1 rGopFla2: GCA_025201965.1
UCSC Genome Browser rGopFla2: GCA_025201925.1 rGopFla2: GCA_025201965.1

metadata.yaml (view) (edit on github)
species:
  common_name: Mexican gopher tortoise
  family:
    name: Testudinidae
  genome_size: 2500000000
  genome_size_method: null
  individuals:
  - short_name: rGopFla2
  name: Gopherus flavomarginatus
  order:
    name: Testudines
  short_name: rGopFla
  taxon_id: 286002
  project: [ vgp ]
CC BY-SA 3.0 Myles Traphagen (wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR rGopFla2 164.62 Gbp 65.85x 286.0 GiB
10x rGopFla2 248.31 Gbp 99.32x 116.6 GiB
Bionano rGopFla2 N/A 263.61x 1.1 GiB
Arima rGopFla2 167.06 Gbp 66.82x 107.3 GiB
Illumina rGopFla1 202.29 Gbp 80.91x 101.8 GiB
rGopFla3 204.29 Gbp 81.72x 101.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.50 Gbp.
Last upload on 10 July 2019.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
rGopFla1 Illumina 202.29 Gbp 80.91x 101.8 GiB
rGopFla2 PacBio CLR 164.62 Gbp 65.85x 286.0 GiB
10x 248.31 Gbp 99.32x 116.6 GiB
Bionano N/A 263.61x 1.1 GiB
Arima 167.06 Gbp 66.82x 107.3 GiB
rGopFla3 Illumina 204.29 Gbp 81.72x 101.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.50 Gbp.
Last upload on 10 July 2019.
Assemblies
Individual 2 Merged Trio Assembly
Version assembly_curated from 2 November 2021
rGopFla2.mat.Y.cur.20211102.fasta.gz (688.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 9 20.04 Mbp 0 380.50 Mbp
20 24 14.55 Mbp 1 303.24 Mbp
30 44 10.72 Mbp 2 288.98 Mbp
40 70 8.31 Mbp 3 218.34 Mbp
50 104 6.57 Mbp 4 162.94 Mbp
60 151 4.44 Mbp 6 117.50 Mbp
70 219 2.97 Mbp 8 93.14 Mbp
80 345 1.35 Mbp 11 53.03 Mbp
90 891 179.53 Kbp 19 25.72 Mbp
100 0 0
0.948x 2488 2.37 Gbp 622 2.46 Gbp
NG based on genome size 2.50 Gbp.
Individual 2 Maternal Assembly
Version assembly_curated from 2 November 2021
rGopFla2.mat.decon.20211102.fasta.gz (730.8 MiB)

Quality: 33.3 errors/Mb (QV=44.77)

Contigs Scaffolds
NG LG Len LG Len
10 9 20.04 Mbp 0 287.59 Mbp
20 24 14.55 Mbp 1 227.32 Mbp
30 44 10.72 Mbp 3 171.48 Mbp
40 70 8.34 Mbp 4 149.18 Mbp
50 104 6.57 Mbp 6 132.09 Mbp
60 150 4.47 Mbp 8 115.58 Mbp
70 218 2.99 Mbp 11 52.22 Mbp
80 343 1.35 Mbp 17 35.52 Mbp
90 875 188.73 Kbp 27 16.80 Mbp
100 4263 36.07 Kbp 492 88.60 Kbp
1.008x 5256 2.52 Gbp 3327 2.63 Gbp
NG based on genome size 2.50 Gbp.
Individual 2 Paternal Assembly
Version assembly_curated from 2 November 2021
rGopFla2.pat.decon.20211102.fasta.gz (723.2 MiB)

Quality: 88.7 errors/Mb (QV=40.52)

Contigs Scaffolds
NG LG Len LG Len
10 10 18.44 Mbp 1 191.19 Mbp
20 26 13.25 Mbp 2 171.70 Mbp
30 49 10.00 Mbp 4 148.32 Mbp
40 76 8.07 Mbp 5 141.10 Mbp
50 111 6.31 Mbp 7 133.54 Mbp
60 157 4.80 Mbp 9 114.44 Mbp
70 219 3.19 Mbp 12 74.30 Mbp
80 338 1.28 Mbp 17 34.95 Mbp
90 933 145.44 Kbp 28 13.65 Mbp
100 0 849 66.83 Kbp
0.987x 4782 2.47 Gbp 2992 2.58 Gbp
NG based on genome size 2.50 Gbp.
Individual 2 Mitochondrial Assembly
Version assembly_MT_rockefeller from 16 December 2019
rGopFla2.MT.20191216.fasta.gz (4.9 KiB)

Quality: not computed
Assembly Metadata
assembly_nhgri_trio_1.6/rGopFla2.yaml (view)
species: Gopherus flavomarginatus
specimen: rGopFla2
projects:
  - VGP orders
release_to: S3
data_location: S3
mito: s3://genomeark/species/Gopherus_flavomarginatus/rGopFla2/assembly_MT_rockefeller/rGopFla2.MT.20191216.fasta.gz
maternal: s3://genomeark/species/Gopherus_flavomarginatus/rGopFla2/assembly_nhgri_trio_1.6/rGopFla2.mat.asm.20210721.fasta.gz
paternal: s3://genomeark/species/Gopherus_flavomarginatus/rGopFla2/assembly_nhgri_trio_1.6/rGopFla2.pat.asm.20210721.fasta.gz
pipeline:
  - TrioCanu in canu 1.8+298 (mat_c0, pat_c0)
  - Arrow wi binned reads (no unknowns) (mat_c1, pat_c1)
  - purge_dups (mat_p1, pat_p1)
  - Added MT on each haplotype
  - scaff10x (mat_s1, pat_s1)
  - Solve (mat_s2, pat_s2)
  - Salsa 2.2 (mat_s3, pat_s3)
  - Arrow wi binned reads (t1)
  - Longranger wi binned reads + Freebayes, Merfin on both haps (t2 - asm.20210721)
stats: |
  Merqury QV mat 40.8, pat 40.5
rGopFla2_metadata.yml (view)
data:
  pacbio:
    data:
    - N50_length (bp): 33097.0
      name: m54307_190403_184421.subreads.bam
      reads: 485861
      yield (bp): 10228844628
    - N50_length (bp): 31041.0
      name: m54307_190404_045842.subreads.bam
      reads: 563118
      yield (bp): 10839133193
    - N50_length (bp): 29336.0
      name: m54307_190404_192705.subreads.bam
      reads: 630264
      yield (bp): 11666796159
    - N50_length (bp): 30243.0
      name: m54307_190405_054135.subreads.bam
      reads: 615889
      yield (bp): 11798013600
    - N50_length (bp): 30788.0
      name: m54306_190405_175042.subreads.bam
      reads: 511128
      yield (bp): 10054026028
    - N50_length (bp): 28833.0
      name: m54307_190405_155618.subreads.bam
      reads: 618669
      yield (bp): 11358323672
    - N50_length (bp): 30934.0
      name: m54306_190406_142046.subreads.bam
      reads: 536130
      yield (bp): 10601291500
    - N50_length (bp): 27341.0
      name: m54307_190406_021106.subreads.bam
      reads: 620788
      yield (bp): 10692705174
    - N50_length (bp): 31005.0
      name: m54306_190406_040526.subreads.bam
      reads: 561194
      yield (bp): 11027525731
    - N50_length (bp): 27959.0
      name: m54307_190406_122536.subreads.bam
      reads: 629805
      yield (bp): 11068718898
    - N50_length (bp): 30858.0
      name: m54306_190407_105112.subreads.bam
      reads: 568152
      yield (bp): 11128145287
    - N50_length (bp): 30836.0
      name: m54306_190407_003613.subreads.bam
      reads: 547750
      yield (bp): 10826379679
    - N50_length (bp): 30272.0
      name: m54306_190407_210635.subreads.bam
      reads: 558238
      yield (bp): 10809087621
    - N50_length (bp): 29136.0
      name: m54307_190406_224006.subreads.bam
      reads: 624662
      yield (bp): 11536236895
    - N50_length (bp): 30796.0
      name: m54306_190408_072149.subreads.bam
      reads: 578433
      yield (bp): 11375868807
    metadata:
    - name: m54307_190403_184421.subreads.bam
      datatype: clr
    - name: m54307_190404_045842.subreads.bam
      datatype: clr
    - name: m54307_190404_192705.subreads.bam
      datatype: clr
    - name: m54307_190405_054135.subreads.bam
      datatype: clr
    - name: m54306_190405_175042.subreads.bam
      datatype: clr
    - name: m54307_190405_155618.subreads.bam
      datatype: clr
    - name: m54306_190406_142046.subreads.bam
      datatype: clr
    - name: m54307_190406_021106.subreads.bam
      datatype: clr
    - name: m54306_190406_040526.subreads.bam
      datatype: clr
    - name: m54307_190406_122536.subreads.bam
      datatype: clr
    - name: m54306_190407_105112.subreads.bam
      datatype: clr
    - name: m54306_190407_003613.subreads.bam
      datatype: clr
    - name: m54306_190407_210635.subreads.bam
      datatype: clr
    - name: m54307_190406_224006.subreads.bam
      datatype: clr
    - name: m54306_190408_072149.subreads.bam
      datatype: clr
    summary:
      yield (bp): 165011096872
      reads: 8650081
      coverage (X): 57.78
  bionano:
    data:
      molecules:
      - name: rGopFla2_Saphyr_DLE1_2678875.bnx.gz
        yield (bp): 480946900000.0
        N50 (kb): 284.6
        density (labels/100kb): 14.99
      cmaps:
      - name: rGopFla2_Saphyr_DLE1_2857688.cmap
        length (Mb): 2586.645
        N50 (Mb): 84.098
    metadata:
    - name: rGopFla2_Saphyr_DLE1_2678875.bnx.gz
      enzyme: DLE1
    summary:
      yield (bp): 480946900000
      coverage (X): 168.4
  hic:
  - no stats found
biosamples:
- common_name: Mexican gopher tortoise
  taxon_Id: '286002'
  bioproject_accession: ''
  organism: Gopherus flavomarginatus
  isolate: rGopFla2
  breed: ''
  dev_stage: juvenile
  sex: ''
  tissue: blood
  biomaterial_provider: University of Arizona
  collection_date: 18-07-31
  collected_by: Taylor Edwards
  birth_date: ''
  birth_location: ''
  lat_lon: 36.88 N 104.97 W
  store_cond: -80C
  treatment: ethanol
  description: Offspring of rGopFla1 and rGopFl3; Chihuahua, Mexico; Captive Bred
    - Turner Ranch, New Mexico
  specimen_voucher: ''
  geo_loc_name: 'USA: Raton, NM'
  tube_id: rGopFla2.BL1
assembly:
- no sw yaml file found
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.