Oryza sativa Japonica vs Triticum aestivum LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum aestivum (Triticum aestivum, IWGSC1+popseq) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. 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: 908,058

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

Uncovered: 292,657,876 out of 374,424,240
Covered: 81,766,364 out of 374,424,240

Uncovered: 3,847,640 out of 34,124,807
Matches: 23,334,363 out of 34,124,807
Mismatches: 6,061,250 out of 34,124,807
Insertions: 881,554 out of 34,124,807

Triticum aestivum

Uncovered: 5,968,165,688 out of 6,378,515,436
Covered: 410,349,748 out of 6,378,515,436

Uncovered: 6,234,881 out of 87,732,694
Matches: 64,951,863 out of 87,732,694
Mismatches: 15,238,170 out of 87,732,694
Insertions: 1,307,780 out of 87,732,694

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 Triticum aestivum
Chunk size 20,000,000 50,100,000
Overlap 10,000 10,000
Group set size 0 50,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}