XENLA Genome
From Marcotte Lab
Genome browser
- XenBase - JGIv6
- NIMR, UK (Mike Gilchrist) - JGIv5(2011oct), JGIv6a(2012nov)
- NIG, Japan (Asao Fujiyama & Masanori Taira) - NIGv2
Genome version
In here, 'N50' is calculated based on the combination of 'Scaffolds' and 'Contigs', so it may be slightly different to official report of 'Scaffolds N50'.
Name | Release Date | Concat. Length (bp) | N50 (bp) | Scaffolds > 10kbp | Remarks |
---|---|---|---|---|---|
JGIv1 | 2010 Dec. | 2.30 Gbp | 8 kbp | 385,933 | Internal Use Only. |
JGIv5 | 2011 Oct. | 2.84 Gbp | 0.28 Mbp | 16,625 | Released in Xenopus PI Meeting. |
JGIv6 | 2012 Jul. | 2.75 Gbp | 0.70 Mbp | 8,426 | Officially released in XenBase. |
JGIv6a | 2012 Jul. | 2.75 Gbp | 0.70 Mbp | 8,426 | Officially released in XenBase; Minor update of JGIv6. |
NIGv1 | 2012 Nov. | 2.88 Gbp | 0.34 Mbp | 14,260 | Original name is 'xl.v1soap'; Internal Use Only. |
NIGv1ap | 2012 Nov. | 3.27 Gbp | 0.17 Mbp | 39,283 | Original name is 'xl.v3ap'(AllPath?); Internal Use Only. |
NIGv1m | 2012 Nov. | 2.84 Gbp | 0.28 Mbp | 82,132 | Original name is 'xl.v5m'; Internal Use Only. |
NIGv2 | 2013 Feb. | 2.89 Gbp | 0.72 Mbp | 5,394 | Original name is 'xl.v2soap'; Internal Use Only. |
NIGv2c | 2013 Feb. | 2.88 Gbp | 0.71 Mbp | 5,377 | Original name is 'xl.v2soap,GapClosed'; Can browse at NIG gbrowser. |
JGIv7a | 2013 Mar. | 2.72 Gbp | 1.15 Mbp | 5,714 | JGI7;Internal Use Only. |
JGIv7b | 2013 May | 2.78 Gbp | 3.49 Mbp | 2,598 | JGI7.2;Internal Use Only. |
J-strain Genomic Data Summary
Whole genome shotgun sequencing, JGI/UC Berkeley, USA
- Illumina mate-pair
Whole genome shotgun sequencing, NIG/U Tokyo, Japan
- Illumina paired-end (207 bp insertion): 1,004 M reads, 105 G bases
- Illumina paired-end (425 bp insertion): 672 M reads, 78 G bases
- Illumina paired-end (900 bp insertion): 695 M reads, 60 G bases
- Illumina mate-pair (1,387 bp insertion): 188 M reads, 15 G bases
- Illumina mate-pair (3,762 bp insertion): 188 M reads, 15 G bases
- Illumina mate-pair (9,850 bp insertion): 239 M reads, 18 G bases
Whole genome shotgun sequencing, UT Austin, USA
- SOLiD v3 mate-pair (1,500 bp insertion): 608 M reads, 30 G bases
Fosmid-end sequencing, JGI/Berkeley + UW, USA
- Illumina paired-end (? bp insertion): 18 M reads, 1.35 G bases
BAC-end sequencing, NIG/U Tokyo, Japan
- Sanger sequencing
- SceI BACs: 720,384 sequences in total. 458,392 sequences with good pairs (233 k pairs; mean length 1,061 bp)
- HindIII BACs: 38,400 sequences in total. 34,044 sequences with good pairs (17 k pairs; mean length 1,125 bp)
Fosmid-end sequencing, NIG/U Tokyo, Japan
- Sanger sequencing
- 119,808 sequences in total. 99,652 sequences with good pairs (50 k pairs; mean length 1,106 bp).
BAC full sequencing, NIG/U Tokyo, Japan
- Sanger sequencing.
- 30 BACs (mean length 112 kb).
Fosmid shotgun sequencing, JGI/Berkeley + UW, USA
- Illumina single-end: 102 M reads, 3.5 G bases
BAC shotgun sequencing, UT Austin, USA
- One plate of CHORI-210 (96 BACs).
- SOLiD v3 mate-pair (2,000 bp insertion): 70 M reads, 3.5 G bases
- SOLiD v3 mate-pair (5,000 bp insertion): 56 M reads, 2.8 G bases
FISH, NIG/U Tokyo, Japan
See Also
XENLA_Transcriptome, XENLA_Proteome