Oryza glaberrima vs Oryza rufipogon LastZ results

Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza glaberrima 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 glaberrimaOryza rufipogon
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 122,297 alignment blocks

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

Uncovered: 51,687,708 out of 285,037,524
Covered: 233,349,816 out of 285,037,524

Uncovered: 260,323 out of 36,404,702
Matches: 35,368,434 out of 36,404,702
Mismatches: 632,837 out of 36,404,702
Insertions: 143,108 out of 36,404,702
Identity over aligned base-pairs: 97.9%

Oryza rufipogon

Uncovered: 118,048,370 out of 338,040,714
Covered: 219,992,344 out of 338,040,714

Uncovered: 7,828,215 out of 42,764,129
Matches: 34,367,684 out of 42,764,129
Mismatches: 457,670 out of 42,764,129
Insertions: 110,560 out of 42,764,129
Identity over aligned base-pairs: 98.4%