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Oryza barthii vs Oryza glumipatula LastZ results

Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) 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

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 151,582 alignment blocks

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

Uncovered: 37,937,893 out of 308,272,304
Covered: 270,334,411 out of 308,272,304

Uncovered: 1,416,709 out of 39,538,509
Matches: 31,987,623 out of 39,538,509
Mismatches: 5,973,946 out of 39,538,509
Insertions: 160,231 out of 39,538,509
Identity over aligned base-pairs: 83.9%

Oryza glumipatula

Uncovered: 125,329,710 out of 372,860,283
Covered: 247,530,573 out of 372,860,283

Uncovered: 4,479,139 out of 41,246,944
Matches: 30,967,729 out of 41,246,944
Mismatches: 5,636,400 out of 41,246,944
Insertions: 163,676 out of 41,246,944
Identity over aligned base-pairs: 84.2%