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Oryza glaberrima vs Oryza nivara LastZ results

Oryza glaberrima (Oryza glaberrima, Oryza_glaberrima_V1) 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 glaberrima 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 glaberrimaOryza nivara
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 107,414 alignment blocks

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

Uncovered: 53,404,425 out of 285,037,524
Covered: 231,633,099 out of 285,037,524

Uncovered: 275,389 out of 36,404,702
Matches: 35,341,663 out of 36,404,702
Mismatches: 653,305 out of 36,404,702
Insertions: 134,345 out of 36,404,702
Identity over aligned base-pairs: 97.8%

Oryza nivara

Uncovered: 120,542,566 out of 337,950,324
Covered: 217,407,758 out of 337,950,324

Uncovered: 7,713,237 out of 42,480,949
Matches: 34,191,757 out of 42,480,949
Mismatches: 470,273 out of 42,480,949
Insertions: 105,682 out of 42,480,949
Identity over aligned base-pairs: 98.3%