Oryza meridionalis vs Oryza glumipatula LastZ results

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) 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 glumipatula
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 226,227 alignment blocks

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

Uncovered: 131,746,191 out of 335,668,232
Covered: 203,922,041 out of 335,668,232

Uncovered: 683,469 out of 35,224,824
Matches: 33,179,701 out of 35,224,824
Mismatches: 1,095,854 out of 35,224,824
Insertions: 265,800 out of 35,224,824
Identity over aligned base-pairs: 96.1%

Oryza glumipatula

Uncovered: 188,686,562 out of 372,860,283
Covered: 184,173,721 out of 372,860,283

Uncovered: 7,238,958 out of 41,246,944
Matches: 32,933,263 out of 41,246,944
Mismatches: 838,076 out of 41,246,944
Insertions: 236,647 out of 41,246,944
Identity over aligned base-pairs: 96.8%