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Oryza glumipatula vs Oryza sativa Japonica Group LastZ results

Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) 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 glumipatula 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 183,304 alignment blocks

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

Uncovered: 123,035,665 out of 372,860,283
Covered: 249,824,618 out of 372,860,283

Uncovered: 1,812,612 out of 41,246,944
Matches: 38,792,854 out of 41,246,944
Mismatches: 512,701 out of 41,246,944
Insertions: 128,777 out of 41,246,944
Identity over aligned base-pairs: 98.4%

Oryza sativa Japonica Group

Uncovered: 90,086,760 out of 375,049,285
Covered: 284,962,525 out of 375,049,285

Uncovered: 485,640 out of 34,818,902
Matches: 33,548,833 out of 34,818,902
Mismatches: 649,657 out of 34,818,902
Insertions: 134,772 out of 34,818,902
Identity over aligned base-pairs: 97.7%

Block size distribution

Size range All 183,304 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,089
12.3 kb
10 bp - 100 bp
37,546
2.2 Mb
19,941
1.2 Mb
100 bp - 1 kb
92,270
33.9 Mb
43,100
15.0 Mb
1 kb - 10 kb
45,139
145.4 Mb
13,821
33.7 Mb
10 kb - 100 kb
6,259
107.0 Mb
248
5.6 Mb
100 kb - 1 Mb
1
131.0 kb
33
6.6 Mb
10 Mb - 100 Mb
12
226.5 Mb