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Oryza sativa Japonica Group vs Arabidopsis lyrata LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

No configuration parameters are available.

Statistics over 82,366 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 346,173,056 out of 375,049,285
Covered: 28,876,229 out of 375,049,285

Uncovered: 16,596,440 out of 34,818,902
Matches: 11,790,326 out of 34,818,902
Mismatches: 6,002,942 out of 34,818,902
Insertions: 429,194 out of 34,818,902
Identity over aligned base-pairs: 64.7%

Arabidopsis lyrata

Uncovered: 187,824,233 out of 206,667,935
Covered: 18,843,702 out of 206,667,935

Uncovered: 22,202,484 out of 35,389,059
Matches: 8,605,523 out of 35,389,059
Mismatches: 4,312,852 out of 35,389,059
Insertions: 268,200 out of 35,389,059
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 82,366 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
624
3.3 kb
10 bp - 100 bp
12,555
853.9 kb
2,394
168.7 kb
100 bp - 1 kb
64,058
21.6 Mb
15,805
6.5 Mb
1 kb - 10 kb
5,129
7.7 Mb
10,839
22.9 Mb
10 kb - 100 kb
43
681.4 kb