Oryza sativa Japonica vs Phaseolus vulgaris LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 141,870

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

Uncovered: 342,160,241 out of 375,049,285
Covered: 32,889,044 out of 375,049,285

Uncovered: 14,298,452 out of 34,403,043
Matches: 12,983,972 out of 34,403,043
Mismatches: 6,603,253 out of 34,403,043
Insertions: 517,366 out of 34,403,043

Phaseolus vulgaris

Uncovered: 488,729,557 out of 521,076,696
Covered: 32,347,139 out of 521,076,696

Uncovered: 12,495,034 out of 34,663,348
Matches: 14,482,977 out of 34,663,348
Mismatches: 7,216,935 out of 34,663,348
Insertions: 468,402 out of 34,663,348

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
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)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Phaseolus vulgaris
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}