Oryza sativa Japonica Group vs Oryza rufipogon LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Japonica 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 Japonica GroupOryza rufipogon
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 103,093 alignment blocks

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

Uncovered: 70,757,579 out of 373,245,519
Covered: 302,487,940 out of 373,245,519

Uncovered: 337,005 out of 44,520,596
Matches: 43,620,233 out of 44,520,596
Mismatches: 445,769 out of 44,520,596
Insertions: 117,589 out of 44,520,596
Identity over aligned base-pairs: 98.7%

Oryza rufipogon

Uncovered: 51,237,990 out of 338,040,714
Covered: 286,802,724 out of 338,040,714

Uncovered: 1,152,224 out of 42,764,129
Matches: 41,374,852 out of 42,764,129
Mismatches: 185,533 out of 42,764,129
Insertions: 51,520 out of 42,764,129
Identity over aligned base-pairs: 99.4%