Oryza barthii vs Oryza glumaepatula LastZ Results

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Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza glumaepatula (Oryza glumaepatula, ALNU02000000) 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: 151,582

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

Uncovered: 37,937,893 out of 308,272,304
Covered: 270,334,411 out of 308,272,304

Uncovered: 1,416,709 out of 39,538,509
Matches: 31,987,623 out of 39,538,509
Mismatches: 5,973,946 out of 39,538,509
Insertions: 160,231 out of 39,538,509

Oryza glumaepatula

Uncovered: 125,329,710 out of 372,860,283
Covered: 247,530,573 out of 372,860,283

Uncovered: 4,479,139 out of 41,246,944
Matches: 30,967,729 out of 41,246,944
Mismatches: 5,636,400 out of 41,246,944
Insertions: 163,676 out of 41,246,944

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)