Arvicanthis niloticus

African grass rat

Included in the VGP.

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


Resource Maternal Assembly Paternal Assembly
GenBank mArvNil1: GCA_011750645.1 mArvNil1: GCA_011762545.1
ENA mArvNil1: GCA_011750645.1 mArvNil1: GCA_011762545.1
UCSC Genome Browser mArvNil1: GCA_011750645.1 mArvNil1: GCA_011762545.1

metadata.yaml (view) (edit on github)
species:
  common_name: African grass rat
  family:
    name: Muridae
  genome_size: 3400000000
  genome_size_method: null
  individuals:
  - short_name: mArvNil1
  name: Arvicanthis niloticus
  order:
    name: Rodentia
  short_name: mArvNil
  taxon_id: 61156
  project: [ vgp ]
Copyright Huishi Toh, used with permission
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR mArvNil1 207.27 Gbp 60.96x 357.1 GiB
10x mArvNil1 261.68 Gbp 76.96x 124.2 GiB
Bionano mArvNil1 N/A 121.92x 838.7 MiB
Arima mArvNil1 223.51 Gbp 65.74x 136.2 GiB
Illumina mArvNil2 241.49 Gbp 71.03x 118.7 GiB
mArvNil3 263.31 Gbp 77.44x 128.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.40 Gbp.
Last upload on 27 July 2019.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mArvNil1 PacBio CLR 207.27 Gbp 60.96x 357.1 GiB
10x 261.68 Gbp 76.96x 124.2 GiB
Bionano N/A 121.92x 838.7 MiB
Arima 223.51 Gbp 65.74x 136.2 GiB
mArvNil2 Illumina 241.49 Gbp 71.03x 118.7 GiB
mArvNil3 Illumina 263.31 Gbp 77.44x 128.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.40 Gbp.
Last upload on 27 July 2019.
Assemblies
Individual 1 Merged Trio Assembly
Version assembly_curated from 16 January 2020
mArvNil1.pat.X.cur.20200116.fasta.gz (713.3 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 38.05 Mbp 2 139.27 Mbp
20 18 23.56 Mbp 4 130.35 Mbp
30 38 13.77 Mbp 7 91.43 Mbp
40 67 9.47 Mbp 11 80.94 Mbp
50 112 5.95 Mbp 16 73.42 Mbp
60 211 1.75 Mbp 22 52.02 Mbp
70 1193 91.15 Kbp 32 6.38 Mbp
80 0 0
90 0 0
100 0 0
0.728x 3219 2.48 Gbp 1595 2.50 Gbp
NG based on genome size 3.40 Gbp.
Individual 1 Maternal Assembly
Version assembly_curated from 3 September 2019
mArvNil1.mat.decon.20190903.fasta.gz (710.9 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 10 25.57 Mbp 2 139.09 Mbp
20 28 16.42 Mbp 4 131.09 Mbp
30 54 11.48 Mbp 8 88.78 Mbp
40 89 7.78 Mbp 12 78.78 Mbp
50 142 5.00 Mbp 16 63.83 Mbp
60 262 1.62 Mbp 23 48.51 Mbp
70 1417 76.53 Kbp 43 0.84 Mbp
80 0 0
90 0 0
100 0 0
0.723x 3136 2.46 Gbp 1610 2.49 Gbp
NG based on genome size 3.40 Gbp.
Individual 1 Paternal Assembly
Version assembly_curated from 3 September 2019
mArvNil1.pat.decon.20190903.fasta.gz (711.2 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 7 38.05 Mbp 1 164.71 Mbp
20 18 23.56 Mbp 3 135.23 Mbp
30 38 13.77 Mbp 6 91.55 Mbp
40 67 9.55 Mbp 11 78.14 Mbp
50 112 5.58 Mbp 15 64.04 Mbp
60 216 1.65 Mbp 22 50.89 Mbp
70 1458 76.79 Kbp 34 4.23 Mbp
80 0 0
90 0 0
100 0 0
0.723x 3303 2.46 Gbp 1740 2.52 Gbp
NG based on genome size 3.40 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 20 August 2019
mArvNil1.MT.20190820.fasta.gz (4.8 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.