Callithrix jacchus

common marmoset

Included in the VGP.

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


Resource Maternal Assembly Paternal Assembly
GenBank mCalJac1: GCA_011078405.1 mCalJac1: GCA_011100535.2
ENA mCalJac1: GCA_011078405.1 mCalJac1: GCA_011100535.2
UCSC Genome Browser mCalJac1: GCA_011078405.1 mCalJac1: GCA_011100535.2

metadata.yaml (view) (edit on github)
species:
  common_name: common marmoset
  family:
    name: Callitrichidae
  genome_size: 3430000000
  genome_size_method: null
  individuals:
  - short_name: mCalJac1
  name: Callithrix jacchus
  order:
    name: Primates
  short_name: mCalJac
  taxon_id: 9483
  project: [ vgp ]
CC BY-SA 2.0 Luciano Marra (flickr)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR mCalJac1 217.82 Gbp 63.50x 378.3 GiB
10x mCalJac1 193.29 Gbp 56.35x 91.5 GiB
Bionano mCalJac1 N/A 154.52x 837.7 MiB
Arima mCalJac1 354.23 Gbp 103.27x 180.3 GiB
Illumina mCalJac2 234.81 Gbp 68.46x 114.0 GiB
mCalJac3 253.41 Gbp 73.88x 123.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.43 Gbp.
Last upload on 28 June 2019.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mCalJac1 PacBio CLR 217.82 Gbp 63.50x 378.3 GiB
10x 193.29 Gbp 56.35x 91.5 GiB
Bionano N/A 154.52x 837.7 MiB
Arima 354.23 Gbp 103.27x 180.3 GiB
mCalJac2 Illumina 234.81 Gbp 68.46x 114.0 GiB
mCalJac3 Illumina 253.41 Gbp 73.88x 123.4 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.43 Gbp.
Last upload on 28 June 2019.
Assemblies
Individual 1 Merged Trio Assembly
Version assembly_curated from 25 April 2021
mCalJac1.pat.X.cur.20210425.fasta.gz (855.4 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 6 35.26 Mbp 1 202.81 Mbp
20 18 24.65 Mbp 3 173.41 Mbp
30 34 18.02 Mbp 5 159.67 Mbp
40 55 14.60 Mbp 7 146.90 Mbp
50 85 9.93 Mbp 10 128.53 Mbp
60 130 5.87 Mbp 13 117.64 Mbp
70 211 3.05 Mbp 16 98.11 Mbp
80 485 361.32 Kbp 21 47.06 Mbp
90 0 0
100 0 0
0.834x 2399 2.86 Gbp 1234 2.87 Gbp
NG based on genome size 3.43 Gbp.
Individual 1 Maternal Assembly
Version assembly_curated from 12 February 2020
mCalJac1.mat.cur.20200212.fasta.gz (809.5 MiB)

Quality: 43.7 errors/Mb (QV=43.60)

Contigs Scaffolds
NG LG Len LG Len
10 10 23.59 Mbp 1 202.58 Mbp
20 27 17.91 Mbp 3 172.75 Mbp
30 51 11.37 Mbp 5 160.12 Mbp
40 84 8.82 Mbp 7 146.90 Mbp
50 131 6.02 Mbp 10 127.66 Mbp
60 205 3.72 Mbp 13 117.27 Mbp
70 330 1.98 Mbp 16 97.94 Mbp
80 688 297.58 Kbp 21 45.74 Mbp
90 0 0
100 0 0
0.816x 1284 2.80 Gbp 216 2.81 Gbp
NG based on genome size 3.43 Gbp.
Individual 1 Paternal Assembly
Version assembly_curated from 25 April 2021
mCalJac1.pat.cur.20210425.fasta.gz (811.7 MiB)

Quality: 81.4 errors/Mb (QV=40.89)

Contigs Scaffolds
NG LG Len LG Len
10 6 35.26 Mbp 1 202.81 Mbp
20 18 24.65 Mbp 3 173.41 Mbp
30 34 18.02 Mbp 5 159.67 Mbp
40 55 14.60 Mbp 7 136.97 Mbp
50 85 9.83 Mbp 10 126.10 Mbp
60 131 5.70 Mbp 13 112.97 Mbp
70 220 2.38 Mbp 16 74.70 Mbp
80 0 0
90 0 0
100 0 0
0.792x 2211 2.72 Gbp 1217 2.73 Gbp
NG based on genome size 3.43 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 20 August 2019
mCalJac1.MT.20190820.fasta.gz (5.0 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.