Oryza sativa Japonica Group vs Ipomoea triloba LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) 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: 159,398

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

Uncovered: 340,566,479 out of 375,049,285
Covered: 34,482,806 out of 375,049,285

Uncovered: 13,780,071 out of 34,424,450
Matches: 13,366,136 out of 34,424,450
Mismatches: 6,729,749 out of 34,424,450
Insertions: 548,494 out of 34,424,450

Ipomoea triloba

Uncovered: 423,876,450 out of 461,827,428
Covered: 37,950,978 out of 461,827,428

Uncovered: 14,687,552 out of 39,533,495
Matches: 16,260,432 out of 39,533,495
Mismatches: 8,015,852 out of 39,533,495
Insertions: 569,659 out of 39,533,495

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 Ipomoea triloba
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}