Oryza meridionalis vs Oryza punctata LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis 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)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza meridionalisOryza punctata
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 297,644 alignment blocks

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

Uncovered: 165,257,598 out of 335,668,232
Covered: 170,410,634 out of 335,668,232

Uncovered: 1,325,841 out of 35,224,824
Matches: 31,035,784 out of 35,224,824
Mismatches: 2,308,770 out of 35,224,824
Insertions: 554,429 out of 35,224,824
Identity over aligned base-pairs: 91.6%

Oryza punctata

Uncovered: 249,625,557 out of 393,816,603
Covered: 144,191,046 out of 393,816,603

Uncovered: 8,041,229 out of 39,315,246
Matches: 29,257,732 out of 39,315,246
Mismatches: 1,657,204 out of 39,315,246
Insertions: 359,081 out of 39,315,246
Identity over aligned base-pairs: 93.6%