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Oryza nivara vs Oryza brachyantha LastZ results

Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza nivara 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

ParameterValue
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)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza nivaraOryza brachyantha
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 262,679 alignment blocks

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

Uncovered: 206,368,317 out of 337,950,324
Covered: 131,582,007 out of 337,950,324

Uncovered: 5,022,538 out of 42,480,949
Matches: 31,757,349 out of 42,480,949
Mismatches: 4,824,584 out of 42,480,949
Insertions: 876,478 out of 42,480,949
Identity over aligned base-pairs: 84.8%

Oryza brachyantha

Uncovered: 143,077,735 out of 250,927,218
Covered: 107,849,483 out of 250,927,218

Uncovered: 2,381,498 out of 30,210,943
Matches: 24,688,350 out of 30,210,943
Mismatches: 2,719,909 out of 30,210,943
Insertions: 421,186 out of 30,210,943
Identity over aligned base-pairs: 88.7%