Arabidopsis thaliana vs Oryza sativa Japonica LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Arabidopsis thaliana 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: 81,291

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 101,090,527 out of 119,667,750
Covered: 18,577,223 out of 119,667,750

Uncovered: 19,827,446 out of 33,462,323
Matches: 8,890,436 out of 33,462,323
Mismatches: 4,468,824 out of 33,462,323
Insertions: 275,617 out of 33,462,323

Oryza sativa Japonica Group

Uncovered: 345,625,867 out of 374,424,240
Covered: 28,798,373 out of 374,424,240

Uncovered: 16,364,338 out of 34,124,807
Matches: 11,482,805 out of 34,124,807
Mismatches: 5,862,754 out of 34,124,807
Insertions: 414,910 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)