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

Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

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: 3,822,079 out of 41,246,944
Matches: 36,774,153 out of 41,246,944
Mismatches: 519,587 out of 41,246,944
Insertions: 131,125 out of 41,246,944
Identity over aligned base-pairs: 98.3%

Oryza sativa Japonica Group

Uncovered: 89,461,715 out of 374,424,240
Covered: 284,962,525 out of 374,424,240

Uncovered: 2,116,270 out of 34,124,807
Matches: 31,243,977 out of 34,124,807
Mismatches: 632,857 out of 34,124,807
Insertions: 131,703 out of 34,124,807
Identity over aligned base-pairs: 97.6%