Oryza sativa Japonica Group vs Leersia perrieri LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Leersia perrieri (Leersia perrieri, Lperr_V1.4) 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 GroupLeersia perrieri
Chunk size30,000,00010,100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 260,363 alignment blocks

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

Uncovered: 227,825,844 out of 373,245,519
Covered: 145,419,675 out of 373,245,519

Uncovered: 4,454,953 out of 44,520,596
Matches: 33,715,443 out of 44,520,596
Mismatches: 5,300,802 out of 44,520,596
Insertions: 1,049,398 out of 44,520,596
Identity over aligned base-pairs: 84.2%

Leersia perrieri

Uncovered: 150,308,343 out of 266,687,832
Covered: 116,379,489 out of 266,687,832

Uncovered: 4,680,218 out of 36,899,367
Matches: 28,018,184 out of 36,899,367
Mismatches: 3,633,392 out of 36,899,367
Insertions: 567,573 out of 36,899,367
Identity over aligned base-pairs: 87.0%