Sturnira parvidens

little yellow-shouldered Mesoamerican bat

Included in the VGP and BAT1K.

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


metadata.yaml (view) (edit on github)
species:
  short_name: mStuPar
  name: Sturnira parvidens
  taxon_id: 196700
  common_name: little yellow-shouldered Mesoamerican bat
  order:
    name: Chiroptera
  family:
    name: Phyllostomidae
  individuals:
    - short_name: mStuPar1
  genome_size: 2704170000
  genome_size_method: GoaT
  project: [ vgp , bat1k ]
No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) mStuPar1 18.67 Gbp 6.90x 62.7 GiB
PacBio HiFi (.bam) mStuPar1 95.06 Gbp 35.15x 319.1 GiB
Arima mStuPar1 149.32 Gbp 55.22x 83.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.70 Gbp.
Last upload on 21 November 2023.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mStuPar1 PacBio HiFi (.fq) 18.67 Gbp 6.90x 62.7 GiB
PacBio HiFi (.bam) 95.06 Gbp 35.15x 319.1 GiB
Arima 149.32 Gbp 55.22x 83.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.70 Gbp.
Last upload on 21 November 2023.
Assemblies
Individual 1 Haplotype 1 Assembly
Version assembly_curated from 8 August 2025
mStuPar1.hap1.cur.20250808.fasta.gz (659.8 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 103.36 Mbp 2 216.38 Mbp
20 6 78.67 Mbp 3 193.61 Mbp
30 9 73.52 Mbp 4 180.14 Mbp
40 14 52.18 Mbp 6 156.56 Mbp
50 21 30.70 Mbp 8 149.30 Mbp
60 31 22.79 Mbp 10 135.56 Mbp
70 46 15.69 Mbp 12 109.06 Mbp
80 75 4.28 Mbp 15 59.52 Mbp
90 0 0
100 0 0
0.871x 1054 2.36 Gbp 947 2.36 Gbp
NG based on genome size 2.70 Gbp.
Individual 1 Haplotype 2 Assembly
Version assembly_curated from 8 August 2025
mStuPar1.hap2.cur.20250808.fasta.gz (553.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 3 105.11 Mbp 2 216.32 Mbp
20 6 84.82 Mbp 3 194.46 Mbp
30 9 67.66 Mbp 4 181.21 Mbp
40 14 50.53 Mbp 6 157.87 Mbp
50 20 34.51 Mbp 8 143.90 Mbp
60 31 18.58 Mbp 10 121.27 Mbp
70 50 10.36 Mbp 12 97.15 Mbp
80 0 0
90 0 0
100 0 0
0.793x 786 2.14 Gbp 703 2.14 Gbp
NG based on genome size 2.70 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 29 November 2023
mStuPar1.MT.20231129.fasta.gz (5.3 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/mStuPar1.yml (view)
species: Sturnira parvidens
specimen: mStuPar1
projects: 
  - vgp
  - bat1k
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
primary: s3://genomeark/species/Sturnira_parvidens/mStuPar1/assembly_vgp_HiC_2.0/mStuPar1.HiC.hap1.20231129.fasta.gz
haplotigs: s3://genomeark/species/Sturnira_parvidens/mStuPar1/assembly_vgp_HiC_2.0/mStuPar1.HiC.hap2.20231129.fasta.gz
pretext: s3://genomeark/species/Sturnira_parvidens/mStuPar1/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/mStuPar1_hap1_s2.pretext
pretext: s3://genomeark/species/Sturnira_parvidens/mStuPar1/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/mStuPar1_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Sturnira_parvidens/mStuPar1/assembly_vgp_HiC_2.0/evaluation/merqury/mStuPar1_png/
pacbio_read_dir: s3://genomeark/species/Sturnira_parvidens/mStuPar1/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Sturnira_parvidens/mStuPar1/genomic_data/arima/
mito: s3://genomeark/species/Sturnira_parvidens/mStuPar1/assembly_MT_rockefeller/mStuPar1.MT.20231129.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of mStuPar1. This hap1 assembly and hap2 assembly underwent separate HiC scaffolding with YaHS. The HiC prep kit used was Swift-IDT. The HiC reaction was using Arima kit v2.
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.