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Oryza punctata vs Oryza sativa Japonica Group LastZ results

Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza punctata 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 843,843 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza punctata

Uncovered: 159,679,307 out of 393,816,603
Covered: 234,137,296 out of 393,816,603

Uncovered: 637,198 out of 39,315,246
Matches: 35,822,060 out of 39,315,246
Mismatches: 2,376,185 out of 39,315,246
Insertions: 479,803 out of 39,315,246
Identity over aligned base-pairs: 92.6%

Oryza sativa Japonica Group

Uncovered: 141,340,696 out of 375,049,285
Covered: 233,708,589 out of 375,049,285

Uncovered: 865,512 out of 34,818,902
Matches: 31,329,697 out of 34,818,902
Mismatches: 2,143,346 out of 34,818,902
Insertions: 480,347 out of 34,818,902
Identity over aligned base-pairs: 92.3%

Block size distribution

Size range All 843,843 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12,990
80.5 kb
10 bp - 100 bp
174,676
10.6 Mb
74,746
4.9 Mb
100 bp - 1 kb
533,844
191.4 Mb
200,917
71.5 Mb
1 kb - 10 kb
121,899
278.6 Mb
45,109
99.5 Mb
10 kb - 100 kb
434
5.2 Mb
737
13.9 Mb
100 kb - 1 Mb
30
5.2 Mb
1 Mb - 10 Mb
10
82.9 Mb
10 Mb - 100 Mb
14
208.0 Mb