Suncus etruscus

white-toothed pygmy shrew

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mSunEtr1: GCA_024139225.1 mSunEtr1: GCA_024140225.1
ENA mSunEtr1: GCA_024139225.1 mSunEtr1: GCA_024140225.1
UCSC Genome Browser mSunEtr1: GCA_024139225.1 mSunEtr1: GCA_024140225.1

metadata.yaml (view) (edit on github)
species:
  short_name: mSunEtr
  name: Suncus etruscus
  taxon_id: 109475
  common_name: white-toothed pygmy shrew
  order:
    name: Eulipotyphla
  family:
    name: Soricidae
  individuals:
    - short_name: mSunEtr1
      sex: male
      provider: Susanne Meyer, Jessica Antosiewicz-Bourget, Yury Bukhman
  genome_size: 3000000000
  genome_size_method:
  project: [ vgp ]
CC BY-NC-SA 2.0 Bernard DUPONT (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR mSunEtr1 429.46 Gbp 143.15x 770.6 GiB
10x mSunEtr1 317.83 Gbp 105.94x 155.1 GiB
Bionano mSunEtr1 N/A 209.49x 857.0 MiB
Arima mSunEtr1 162.67 Gbp 54.22x 100.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.00 Gbp.
Last upload on 27 May 2021.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mSunEtr1 PacBio CLR 429.46 Gbp 143.15x 770.6 GiB
10x 317.83 Gbp 105.94x 155.1 GiB
Bionano N/A 209.49x 857.0 MiB
Arima 162.67 Gbp 54.22x 100.8 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.00 Gbp.
Last upload on 27 May 2021.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 25 November 2021
mSunEtr1.pri.cur.20211125.fasta.gz (705.6 MiB)

Quality: 177.7 errors/Mb (QV=37.50)

Contigs Scaffolds
NG LG Len LG Len
10 13 16.00 Mbp 1 171.22 Mbp
20 38 9.94 Mbp 3 168.49 Mbp
30 76 6.71 Mbp 5 137.51 Mbp
40 127 5.22 Mbp 7 131.95 Mbp
50 193 3.86 Mbp 9 116.30 Mbp
60 285 2.78 Mbp 12 104.75 Mbp
70 420 1.79 Mbp 15 93.47 Mbp
80 705 484.96 Kbp 19 44.86 Mbp
90 0 0
100 0 0
0.820x 1158 2.46 Gbp 148 2.47 Gbp
NG based on genome size 3.00 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 25 November 2021
mSunEtr1.alt.cur.20211125.fasta.gz (434.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 634 317.43 Kbp 634 317.43 Kbp
20 1922 181.66 Kbp 1921 181.98 Kbp
30 4046 112.35 Kbp 4041 112.70 Kbp
40 7488 67.97 Kbp 7476 68.11 Kbp
50 14023 24.63 Kbp 14000 24.72 Kbp
60 0 0
70 0 0
80 0 0
90 0 0
100 0 0
0.505x 14841 1.52 Gbp 14815 1.52 Gbp
NG based on genome size 3.00 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 27 May 2021
mSunEtr1.MT.20210527.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_1.7/mSunEtr1.yaml (view)
species: Suncus_etruscus
specimen: mSunEtr1
projects:
  - vgp
primary: s3://genomeark/species/Suncus_etruscus/mSunEtr1/assembly_vgp_standard_1.7/mSunEtr1.pri.asm.20210809.fasta.gz
haplotigs: s3://genomeark/species/Suncus_etruscus/mSunEtr1/assembly_vgp_standard_1.7/mSunEtr1.alt.asm.20210809.fasta.gz
mito: s3://genomeark/species/Suncus_etruscus/mSunEtr1/assembly_MT_rockefeller/mSunEtr1.MT.20210527.fasta.gz
hic_bam: s3://genomeark/species/Suncus_etruscus/mSunEtr1/assembly_vgp_standard_1.7/evaluation/pretext/mSunEtr1.pri.asm.20210809.fasta.gz.bam
pretext: s3://genomeark/species/Suncus_etruscus/mSunEtr1/assembly_vgp_standard_1.7/evaluation/pretext/mSunEtr1.pri.asm.20210809.fasta.gz.pretext
kmer_spectra_img: s3://genomeark/species/Suncus_etruscus/mSunEtr1/assembly_vgp_standard_1.7/evaluation/merqury/
pipeline:
  - falcon (2.0.2)
  - falcon_unzip (8.0.1)
  - purge_dups (1.0.0)
  - scaff10x (2.0.3)
  - bionano_solve (Solve3.4.0)
  - salsa (v2.2)
  - gcpp (2.0.2)
  - merfin (1.0)
  - freebayes (1.3.1)
  
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.