Oryza sativa Indica Group vs Oryza nivara LastZ results

Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) 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 sativa Indica Group 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 sativa Indica GroupOryza nivara
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 111,986 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Indica Group

Uncovered: 75,026,722 out of 374,545,499
Covered: 299,518,777 out of 374,545,499

Uncovered: 300,898 out of 42,733,995
Matches: 41,789,761 out of 42,733,995
Mismatches: 540,351 out of 42,733,995
Insertions: 102,985 out of 42,733,995
Identity over aligned base-pairs: 98.5%

Oryza nivara

Uncovered: 68,500,490 out of 337,950,324
Covered: 269,449,834 out of 337,950,324

Uncovered: 2,086,818 out of 42,480,949
Matches: 40,016,448 out of 42,480,949
Mismatches: 306,709 out of 42,480,949
Insertions: 70,974 out of 42,480,949
Identity over aligned base-pairs: 99.1%