Oryza sativa Japonica Group vs Cucumis melo LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cucumis melo (Cucumis melo, Melonv4) 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: 125,664

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

Uncovered: 344,748,898 out of 375,049,285
Covered: 30,300,387 out of 375,049,285

Uncovered: 15,541,419 out of 34,424,450
Matches: 12,240,831 out of 34,424,450
Mismatches: 6,234,026 out of 34,424,450
Insertions: 408,174 out of 34,424,450

Cucumis melo

Uncovered: 331,434,842 out of 357,857,370
Covered: 26,422,528 out of 357,857,370

Uncovered: 11,224,275 out of 27,459,425
Matches: 10,577,049 out of 27,459,425
Mismatches: 5,325,022 out of 27,459,425
Insertions: 333,079 out of 27,459,425

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 melo
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 10,100,000 10,100,000
Masking options