Oryza sativa Japonica Group vs Oryza glaberrima LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. Oryza sativa Japonica Group 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 sativa Japonica GroupOryza glaberrima
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 183,406 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 104,102,970 out of 374,424,240
Covered: 270,321,270 out of 374,424,240

Uncovered: 1,592,815 out of 34,124,807
Matches: 31,069,594 out of 34,124,807
Mismatches: 1,255,998 out of 34,124,807
Insertions: 206,400 out of 34,124,807
Identity over aligned base-pairs: 95.5%

Oryza glaberrima

Uncovered: 88,192,351 out of 316,419,574
Covered: 228,227,223 out of 316,419,574

Uncovered: 4,000,029 out of 36,293,721
Matches: 31,972,353 out of 36,293,721
Mismatches: 268,429 out of 36,293,721
Insertions: 52,910 out of 36,293,721
Identity over aligned base-pairs: 99.0%