Oryza meridionalis vs Oryza nivara LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) 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 nivara
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 221,393 alignment blocks

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

Uncovered: 129,845,880 out of 335,668,232
Covered: 205,822,352 out of 335,668,232

Uncovered: 577,308 out of 35,224,824
Matches: 33,396,355 out of 35,224,824
Mismatches: 1,003,963 out of 35,224,824
Insertions: 247,198 out of 35,224,824
Identity over aligned base-pairs: 96.4%

Oryza nivara

Uncovered: 150,799,068 out of 337,950,324
Covered: 187,151,256 out of 337,950,324

Uncovered: 7,838,195 out of 42,562,444
Matches: 33,656,225 out of 42,562,444
Mismatches: 834,438 out of 42,562,444
Insertions: 233,586 out of 42,562,444
Identity over aligned base-pairs: 96.9%