Oryza rufipogon vs Oryza punctata LastZ results

Oryza rufipogon (Oryza rufipogon, OR_W1943) and Oryza punctata (Oryza punctata, Oryza_punctata_v1.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza rufipogon 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 rufipogonOryza punctata
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 364,762 alignment blocks

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

Uncovered: 139,479,600 out of 338,040,714
Covered: 198,561,114 out of 338,040,714

Uncovered: 1,707,062 out of 42,764,129
Matches: 37,341,610 out of 42,764,129
Mismatches: 3,006,169 out of 42,764,129
Insertions: 709,288 out of 42,764,129
Identity over aligned base-pairs: 91.0%

Oryza punctata

Uncovered: 229,098,676 out of 393,816,603
Covered: 164,717,927 out of 393,816,603

Uncovered: 4,404,512 out of 39,208,571
Matches: 32,573,334 out of 39,208,571
Mismatches: 1,830,464 out of 39,208,571
Insertions: 400,261 out of 39,208,571
Identity over aligned base-pairs: 93.6%