Oryza sativa Japonica vs Musa acuminata LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Musa acuminata (Musa acuminata subsp. malaccensis, MA1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Japonica 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: 113,251

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 334,810,010 out of 374,424,240
Covered: 39,614,230 out of 374,424,240

Uncovered: 10,040,575 out of 34,124,807
Matches: 16,405,846 out of 34,124,807
Mismatches: 7,002,088 out of 34,124,807
Insertions: 676,298 out of 34,124,807

Musa acuminata subsp. malaccensis

Uncovered: 444,986,636 out of 472,960,417
Covered: 27,973,781 out of 472,960,417

Uncovered: 19,900,890 out of 37,920,568
Matches: 12,458,091 out of 37,920,568
Mismatches: 5,139,140 out of 37,920,568
Insertions: 422,447 out of 37,920,568

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)