Oryza barthii vs Oryza sativa Japonica Group LastZ results

Oryza barthii (Oryza barthii, O.barthii_v1) 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 barthii 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 313,253 alignment blocks

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

Uncovered: 29,707,290 out of 308,272,304
Covered: 278,565,014 out of 308,272,304

Uncovered: 1,324,190 out of 39,538,509
Matches: 32,148,806 out of 39,538,509
Mismatches: 5,918,002 out of 39,538,509
Insertions: 147,511 out of 39,538,509
Identity over aligned base-pairs: 84.1%

Oryza sativa Japonica Group

Uncovered: 82,315,766 out of 374,424,240
Covered: 292,108,474 out of 374,424,240

Uncovered: 1,508,710 out of 34,124,807
Matches: 27,132,159 out of 34,124,807
Mismatches: 5,261,628 out of 34,124,807
Insertions: 222,310 out of 34,124,807
Identity over aligned base-pairs: 83.2%