Oryza sativa Japonica vs Leersia perrieri LastZ Results

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Oryza sativa Japonica (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 75. Oryza sativa Japonica was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 260,363

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

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

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Leersia perrieri
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}