Oryza sativa Japonica Group vs Triticum turgidum LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum turgidum (Triticum turgidum, Svevo.v1) 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: 671,091

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

Uncovered: 290,020,848 out of 375,049,285
Covered: 85,028,437 out of 375,049,285

Uncovered: 3,152,204 out of 34,424,450
Matches: 24,155,722 out of 34,424,450
Mismatches: 6,235,839 out of 34,424,450
Insertions: 880,685 out of 34,424,450

Triticum turgidum

Uncovered: 10,182,497,900 out of 10,463,058,104
Covered: 280,560,204 out of 10,463,058,104

Uncovered: 8,310,617 out of 88,577,667
Matches: 61,802,295 out of 88,577,667
Mismatches: 16,600,913 out of 88,577,667
Insertions: 1,863,842 out of 88,577,667

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 Triticum turgidum
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}