Oryza meridionalis vs Oryza brachyantha LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis 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 meridionalisOryza brachyantha
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 244,580 alignment blocks

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

Uncovered: 216,576,784 out of 335,668,232
Covered: 119,091,448 out of 335,668,232

Uncovered: 4,003,058 out of 35,224,824
Matches: 26,670,824 out of 35,224,824
Mismatches: 3,839,766 out of 35,224,824
Insertions: 711,176 out of 35,224,824
Identity over aligned base-pairs: 85.4%

Oryza brachyantha

Uncovered: 163,290,928 out of 260,838,168
Covered: 97,547,240 out of 260,838,168

Uncovered: 6,658,534 out of 33,473,466
Matches: 23,709,343 out of 33,473,466
Mismatches: 2,693,609 out of 33,473,466
Insertions: 411,980 out of 33,473,466
Identity over aligned base-pairs: 88.4%