Rhinatrema bivittatum

two-lined caecilian

Included in the VGP.

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


Resource Primary Assembly Alternate Assembly
GenBank aRhiBiv1: GCA_901001135.2 aRhiBiv1: GCA_901001175.1
ENA aRhiBiv1: GCA_901001135.2 aRhiBiv1: GCA_901001175.1
UCSC Genome Browser aRhiBiv1: GCA_901001135.2 aRhiBiv1: GCA_901001175.1

metadata.yaml (view) (edit on github)
species:
  short_name: aRhiBiv
  name: Rhinatrema bivittatum
  taxon_id: 194408
  common_name: two-lined caecilian
  order:
    name: Apoda
  family:
    name: Rhinatrematidae
  individuals:
    - short_name: aRhiBiv1
      biosample_id: SAMEA104387956
      sex:
  genome_size: 5067838282
  genome_size_method: genomescope k=31
  project: [ vgp ]
Copyright Stuart V Nielsen, used with permission
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio CLR aRhiBiv1 232.06 Gbp 45.79x 415.7 GiB
10x aRhiBiv1 367.47 Gbp 72.51x 250.4 GiB
Bionano aRhiBiv1 N/A 359.44x 1.5 GiB
Arima aRhiBiv1 367.47 Gbp 72.51x 222.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 5.07 Gbp.
Last upload on 1 May 2018.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
aRhiBiv1 PacBio CLR 232.06 Gbp 45.79x 415.7 GiB
10x 367.47 Gbp 72.51x 250.4 GiB
Bionano N/A 359.44x 1.5 GiB
Arima 367.47 Gbp 72.51x 222.5 GiB
Bases and Coverage are approximate.
Coverage based on genome size 5.07 Gbp.
Last upload on 1 May 2018.
Assemblies
Individual 1 Primary Assembly
Version assembly_curated from 9 April 2019
aRhiBiv1.pri.cur.20190409.fasta.gz (1.5 GiB)

Quality: 152.0 errors/Mb (QV=38.18)

Contigs Scaffolds
NG LG Len LG Len
10 48 8.64 Mbp 0 0.84 Gbp
20 117 6.48 Mbp 1 0.83 Gbp
30 206 5.07 Mbp 1 0.83 Gbp
40 318 4.08 Mbp 2 0.60 Gbp
50 455 3.35 Mbp 3 486.88 Mbp
60 623 2.70 Mbp 4 387.03 Mbp
70 838 2.05 Mbp 6 313.51 Mbp
80 1128 1.49 Mbp 7 277.53 Mbp
90 1560 0.89 Mbp 10 103.41 Mbp
100 2556 254.22 Kbp 16 63.94 Mbp
1.043x 4902 5.29 Gbp 1329 5.32 Gbp
NG based on genome size 5.07 Gbp.
Individual 1 Alternate Assembly
Version assembly_curated from 9 April 2019
aRhiBiv1.alt.cur.20190409.fasta.gz (1.3 GiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 545 0.72 Mbp 545 0.72 Mbp
20 1391 0.51 Mbp 1391 0.51 Mbp
30 2523 392.37 Kbp 2523 392.37 Kbp
40 4006 299.18 Kbp 4006 299.18 Kbp
50 5940 231.02 Kbp 5940 231.02 Kbp
60 8452 176.28 Kbp 8452 176.28 Kbp
70 11779 131.49 Kbp 11779 131.49 Kbp
80 16417 89.74 Kbp 16417 89.74 Kbp
90 24732 32.97 Kbp 24732 32.97 Kbp
100 0 0
0.911x 27233 4.62 Gbp 27231 4.62 Gbp
NG based on genome size 5.07 Gbp.
Individual 1 Mitochondrial Assembly
Version assembly_MT_rockefeller from 3 October 2019
aRhiBiv1.MT.20191003.fasta.gz (5.3 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.