Oryza sativa Japonica Group vs Cucumis sativus LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cucumis sativus (Cucumis sativus, ASM407v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 115,125

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

Uncovered: 345,233,330 out of 375,049,285
Covered: 29,815,955 out of 375,049,285

Uncovered: 15,645,329 out of 34,403,043
Matches: 12,142,720 out of 34,403,043
Mismatches: 6,207,610 out of 34,403,043
Insertions: 407,384 out of 34,403,043

Cucumis sativus

Uncovered: 169,672,768 out of 193,829,320
Covered: 24,156,552 out of 193,829,320

Uncovered: 9,552,542 out of 26,192,424
Matches: 10,843,103 out of 26,192,424
Mismatches: 5,462,584 out of 26,192,424
Insertions: 334,195 out of 26,192,424

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 Group Cucumis sativus
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}