Oryza barthii vs Oryza punctata LastZ Results

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Oryza barthii (Oryza barthii, O.barthii_v1) and Oryza punctata (Oryza punctata, AVCL00000000) 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: 825,291

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

Uncovered: 95,930,790 out of 308,272,304
Covered: 212,341,514 out of 308,272,304

Uncovered: 1,335,801 out of 39,538,509
Matches: 30,205,639 out of 39,538,509
Mismatches: 7,329,146 out of 39,538,509
Insertions: 667,923 out of 39,538,509

Oryza punctata

Uncovered: 160,376,751 out of 393,816,603
Covered: 233,439,852 out of 393,816,603

Uncovered: 978,721 out of 39,315,246
Matches: 30,361,028 out of 39,315,246
Mismatches: 7,404,917 out of 39,315,246
Insertions: 570,580 out of 39,315,246

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)