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Oryza nivara vs Oryza barthii LastZ results

Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) and Oryza barthii (Oryza barthii, O.barthii_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza nivara 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

ParameterValue
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)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Statistics over 144,936 alignment blocks

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

Uncovered: 85,825,558 out of 337,950,324
Covered: 252,124,766 out of 337,950,324

Uncovered: 5,032,396 out of 42,562,444
Matches: 31,595,227 out of 42,562,444
Mismatches: 5,771,819 out of 42,562,444
Insertions: 163,002 out of 42,562,444
Identity over aligned base-pairs: 84.2%

Oryza barthii

Uncovered: 34,695,954 out of 308,272,304
Covered: 273,576,350 out of 308,272,304

Uncovered: 1,284,606 out of 39,538,509
Matches: 32,159,338 out of 39,538,509
Mismatches: 5,945,290 out of 39,538,509
Insertions: 149,275 out of 39,538,509
Identity over aligned base-pairs: 84.1%