Oryza barthii vs Oryza sativa Indica LastZ Results

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Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) 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: 155,241

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

Uncovered: 35,135,584 out of 308,272,304
Covered: 273,136,720 out of 308,272,304

Uncovered: 1,095,205 out of 39,538,509
Matches: 32,254,026 out of 39,538,509
Mismatches: 6,027,410 out of 39,538,509
Insertions: 161,868 out of 39,538,509

Oryza sativa Indica Group

Uncovered: 174,817,854 out of 427,004,890
Covered: 252,187,036 out of 427,004,890

Uncovered: 9,520,625 out of 45,465,969
Matches: 30,268,255 out of 45,465,969
Mismatches: 5,530,585 out of 45,465,969
Insertions: 146,504 out of 45,465,969

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)