Sciurus carolinensis

grey squirrel

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mSciCar1: GCA_902686445.2 mSciCar1: GCA_902685475.1
ENA mSciCar1: GCA_902686445.2 mSciCar1: GCA_902685475.1
UCSC Genome Browser mSciCar1: GCA_902686445.2 mSciCar1: GCA_902685475.1

metadata.yaml (view) (edit on github)
species:
  short_name: mSciCar
  name: Sciurus carolinensis
  taxon_id: 30640
  common_name: grey squirrel
  order:
    name: Rodentia
  family:
    name: Sciuridae
  individuals:
    - short_name: mSciCar1
      biosample_id: SAMEA994726
      sex: male
  genome_size:
  genome_size_method:
  project: [ vgp ]
CC BY 2.0, Judy Gallagher (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR mSciCar1 222.76 Gbp 79.12x 381.9 GiB
10x mSciCar1 270.69 Gbp 96.14x 167.2 GiB
Dovetail Genomics mSciCar1 370.23 Gbp 131.50x 237.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.82 Gbp.
Last upload on 8 August 2019.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mSciCar1 PacBio CLR 222.76 Gbp 79.12x 381.9 GiB
10x 270.69 Gbp 96.14x 167.2 GiB
Dovetail Genomics 370.23 Gbp 131.50x 237.3 GiB
Bases and Coverage are approximate.
Coverage based on genome size 2.82 Gbp.
Last upload on 8 August 2019.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 14 November 2019
mSciCar1.pri.cur.20191114.fasta.gz (818.7 MiB)

Quality: 128.4 errors/Mb (QV=38.91)

Contigs Scaffolds
NG LG Len LG Len
10 5 44.40 Mbp 1 199.83 Mbp
20 12 35.14 Mbp 2 183.55 Mbp
30 22 25.19 Mbp 4 175.91 Mbp
40 34 20.21 Mbp 6 154.99 Mbp
50 51 13.98 Mbp 7 148.23 Mbp
60 74 10.81 Mbp 9 140.98 Mbp
70 106 6.73 Mbp 12 118.65 Mbp
80 170 2.83 Mbp 14 88.65 Mbp
90 423 479.98 Kbp 19 30.99 Mbp
100 2575 3.80 Kbp 751 10.39 Kbp
1.000x 2576 2.81 Gbp 752 2.82 Gbp
NG based on genome size 2.82 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 14 November 2019
mSciCar1.alt.cur.20191114.fasta.gz (599.5 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 100 1.58 Mbp 100 1.58 Mbp
20 253 1.15 Mbp 253 1.15 Mbp
30 455 0.88 Mbp 455 0.88 Mbp
40 725 0.66 Mbp 725 0.66 Mbp
50 1081 492.51 Kbp 1081 492.51 Kbp
60 1579 349.54 Kbp 1579 349.58 Kbp
70 2328 218.26 Kbp 2328 218.33 Kbp
80 3509 140.64 Kbp 3508 140.64 Kbp
90 5377 85.88 Kbp 5376 85.91 Kbp
100 9509 1.04 Kbp 9507 1.04 Kbp
1.000x 9510 2.06 Gbp 9508 2.06 Gbp
NG based on genome size 2.82 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 16 December 2019
mSciCar1.MT.20191216.fasta.gz (4.9 KiB)

Quality: not computed
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.