Oryza sativa Indica Group vs Oryza rufipogon LastZ results

Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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 rufipogon
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 146,284 alignment blocks

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

Uncovered: 76,144,342 out of 374,545,499
Covered: 298,401,157 out of 374,545,499

Uncovered: 266,217 out of 42,733,995
Matches: 41,714,102 out of 42,733,995
Mismatches: 624,432 out of 42,733,995
Insertions: 129,244 out of 42,733,995
Identity over aligned base-pairs: 98.2%

Oryza rufipogon

Uncovered: 70,255,676 out of 338,040,714
Covered: 267,785,038 out of 338,040,714

Uncovered: 2,387,324 out of 42,764,129
Matches: 39,918,141 out of 42,764,129
Mismatches: 365,536 out of 42,764,129
Insertions: 93,128 out of 42,764,129
Identity over aligned base-pairs: 98.9%