Oryza sativa Japonica vs Oryza sativa Indica LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 127,294

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

Uncovered: 64,351,985 out of 374,424,240
Covered: 310,072,255 out of 374,424,240

Uncovered: 270,394 out of 34,124,807
Matches: 33,318,603 out of 34,124,807
Mismatches: 446,546 out of 34,124,807
Insertions: 89,264 out of 34,124,807

Oryza sativa Indica Group

Uncovered: 143,812,226 out of 427,004,890
Covered: 283,192,664 out of 427,004,890

Uncovered: 6,417,323 out of 45,465,969
Matches: 38,706,848 out of 45,465,969
Mismatches: 277,779 out of 45,465,969
Insertions: 64,019 out of 45,465,969

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 Oryza sativa Indica
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}