Oryza barthii vs Oryza sativa Japonica LastZ Results

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Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza barthii 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: 313,253

Genome coverage (bp) Coding exon coverage (bp)
Oryza barthii

Uncovered: 29,707,290 out of 308,272,304
Covered: 278,565,014 out of 308,272,304

Uncovered: 1,324,190 out of 39,538,509
Matches: 32,148,806 out of 39,538,509
Mismatches: 5,918,002 out of 39,538,509
Insertions: 147,511 out of 39,538,509

Oryza sativa Japonica Group

Uncovered: 82,315,766 out of 374,424,240
Covered: 292,108,474 out of 374,424,240

Uncovered: 1,508,710 out of 34,124,807
Matches: 27,132,159 out of 34,124,807
Mismatches: 5,261,628 out of 34,124,807
Insertions: 222,310 out of 34,124,807

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)