In this section

Oryza glumipatula vs Oryza nivara LastZ results

Oryza glumipatula (Oryza glumipatula, Oryza_glumaepatula_v1.5) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 75. Oryza glumipatula 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 glumipatulaOryza nivara
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 132,339 alignment blocks

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

Uncovered: 113,922,314 out of 372,860,283
Covered: 258,937,969 out of 372,860,283

Uncovered: 350,759 out of 41,162,840
Matches: 39,850,744 out of 41,162,840
Mismatches: 789,326 out of 41,162,840
Insertions: 172,011 out of 41,162,840
Identity over aligned base-pairs: 97.6%

Oryza nivara

Uncovered: 93,879,033 out of 337,950,324
Covered: 244,071,291 out of 337,950,324

Uncovered: 3,254,201 out of 42,480,949
Matches: 38,552,111 out of 42,480,949
Mismatches: 545,369 out of 42,480,949
Insertions: 129,268 out of 42,480,949
Identity over aligned base-pairs: 98.3%