Oryza sativa Japonica Group vs Oryza brachyantha LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) 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 brachyantha
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 306,220 alignment blocks

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

Uncovered: 227,195,328 out of 374,424,240
Covered: 147,228,912 out of 374,424,240

Uncovered: 2,547,731 out of 34,124,807
Matches: 27,115,006 out of 34,124,807
Mismatches: 3,804,817 out of 34,124,807
Insertions: 657,253 out of 34,124,807
Identity over aligned base-pairs: 85.9%

Oryza brachyantha

Uncovered: 150,356,678 out of 260,838,168
Covered: 110,481,490 out of 260,838,168

Uncovered: 4,128,231 out of 33,473,466
Matches: 25,976,721 out of 33,473,466
Mismatches: 2,927,024 out of 33,473,466
Insertions: 441,490 out of 33,473,466
Identity over aligned base-pairs: 88.5%