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Oryza punctata vs Oryza sativa Indica Group LastZ results

Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza punctata 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 425,040 alignment blocks

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

Uncovered: 164,012,351 out of 393,816,603
Covered: 229,804,252 out of 393,816,603

Uncovered: 868,351 out of 39,315,246
Matches: 35,538,657 out of 39,315,246
Mismatches: 2,435,143 out of 39,315,246
Insertions: 473,095 out of 39,315,246
Identity over aligned base-pairs: 92.4%

Oryza sativa Indica Group

Uncovered: 259,435,284 out of 427,004,890
Covered: 167,569,606 out of 427,004,890

Uncovered: 11,069,337 out of 45,465,969
Matches: 32,050,607 out of 45,465,969
Mismatches: 1,895,344 out of 45,465,969
Insertions: 450,681 out of 45,465,969
Identity over aligned base-pairs: 93.2%