Macropus eugenii

tammar wallaby

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank mMacEug1: GCA_028372415.1 mMacEug1: GCA_028389975.1
ENA mMacEug1: GCA_028372415.1 mMacEug1: GCA_028389975.1
UCSC Genome Browser mMacEug1: GCA_028372415.1 mMacEug1: GCA_028389975.1

metadata.yaml (view) (edit on github)
species:
  short_name: mMacEug
  name: Macropus eugenii
  taxon_id: 9315
  common_name: tammar wallaby
  order:
    name: Diprotodontia
  family:
    name: Macropodidae
  individuals:
    - short_name: mMacEug1
      sex: male
      provider: Andrew Veale
  genome_size: 3000000000
  genome_size_method:
  project: [ vgp ]
CC BY-SA 3.0 DiverDave (Wikimedia)
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (subreads) mMacEug1 1050.47 Gbp 350.16x 2.1 TiB
PacBio HiFi (.fq) mMacEug1 91.20 Gbp 30.40x 69.3 GiB
PacBio HiFi (.bam) mMacEug1 76.08 Gbp 25.36x 227.0 GiB
Bionano mMacEug1 N/A 328.47x 2.1 GiB
Arima mMacEug1 350.86 Gbp 116.95x 220.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.00 Gbp.
Last upload on 3 May 2022.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
mMacEug1 PacBio HiFi (subreads) 1050.47 Gbp 350.16x 2.1 TiB
PacBio HiFi (.fq) 91.20 Gbp 30.40x 69.3 GiB
PacBio HiFi (.bam) 76.08 Gbp 25.36x 227.0 GiB
Bionano N/A 328.47x 2.1 GiB
Arima 350.86 Gbp 116.95x 220.9 GiB
Bases and Coverage are approximate.
Coverage based on genome size 3.00 Gbp.
Last upload on 3 May 2022.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 3 January 2023
mMacEug1.pri.cur.20230103.fasta.gz (0.9 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 5 51.02 Mbp 0 0.76 Gbp
20 11 42.35 Mbp 0 0.76 Gbp
30 20 30.09 Mbp 1 0.54 Gbp
40 31 23.17 Mbp 1 0.54 Gbp
50 46 17.93 Mbp 2 489.67 Mbp
60 64 14.55 Mbp 3 478.17 Mbp
70 87 12.09 Mbp 3 478.17 Mbp
80 116 8.89 Mbp 4 461.86 Mbp
90 156 6.47 Mbp 4 461.86 Mbp
100 211 4.48 Mbp 5 389.61 Mbp
1.147x 829 3.44 Gbp 314 3.45 Gbp
NG based on genome size 3.00 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 29 April 2022
mMacEug1.alt.cur.20220429.fasta.gz (529.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 241 0.84 Mbp 241 0.84 Mbp
20 689 0.55 Mbp 689 0.55 Mbp
30 1363 366.05 Kbp 1363 366.05 Kbp
40 2424 215.27 Kbp 2424 215.27 Kbp
50 4676 79.81 Kbp 4676 79.81 Kbp
60 12266 23.38 Kbp 12266 23.38 Kbp
70 0 0
80 0 0
90 0 0
100 0 0
0.613x 14285 1.84 Gbp 14283 1.84 Gbp
NG based on genome size 3.00 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 17 June 2022
mMacEug1.MT.20220617.fasta.gz (5.0 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_standard_2.0/mMacEug1.yaml (view)
species: Macropus_eugenii
specimen: mMacEug1
projects:
- vgl 
primary:
  s3://genomeark/species/Macropus_eugenii/mMacEug1/assembly_vgp_standard_2.0/mMacEug1.pri.asm.20211109.fasta.gz
haplotigs:
  s3://genomeark/species/Macropus_eugenii/mMacEug1/assembly_vgp_standard_2.0/mMacEug1.alt.asm.20211109.fasta.gz
hic_bam:
  s3://genomeark/species/Macropus_eugenii/mMacEug1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mMacEug1_s2.bam
pretext:
  s3://genomeark/species/Macropus_eugenii/mMacEug1/assembly_vgp_standard_2.0/evaluation/pretext/s2/mMacEug1_s2.bam
kmer_spectra_img:
  s3://genomeark/species/Macropus_eugenii/mMacEug1/assembly_vgp_standard_2.0/evaluation/merqury/p/output_merqury_p.spectra-cn.fl

pipeline:
  - hifiasm (0.15.4+galaxy)
  - purge_dups (1.2.5+galaxy3)
  - bionano_solve (3.6.1+galaxy2)
  - salsa (2.3+galaxy0)
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.