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Oryza punctata vs Oryza glaberrima LastZ results

Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) and Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) 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 403,125 alignment blocks

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

Uncovered: 177,945,609 out of 393,816,603
Covered: 215,870,994 out of 393,816,603

Uncovered: 2,349,575 out of 39,315,246
Matches: 33,518,919 out of 39,315,246
Mismatches: 2,931,947 out of 39,315,246
Insertions: 514,805 out of 39,315,246
Identity over aligned base-pairs: 90.7%

Oryza glaberrima

Uncovered: 169,858,164 out of 316,419,574
Covered: 146,561,410 out of 316,419,574

Uncovered: 7,345,686 out of 36,293,721
Matches: 27,086,442 out of 36,293,721
Mismatches: 1,510,228 out of 36,293,721
Insertions: 351,365 out of 36,293,721
Identity over aligned base-pairs: 93.6%