Triticum aestivum vs Oryza sativa Japonica Group LastZ Results

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Triticum aestivum (Triticum aestivum, IWGSC) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Triticum aestivum 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: 1,354,149

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 13,961,074,617 out of 14,547,261,565
Covered: 586,186,948 out of 14,547,261,565

Uncovered: 12,047,551 out of 136,655,258
Matches: 96,121,876 out of 136,655,258
Mismatches: 25,678,140 out of 136,655,258
Insertions: 2,807,691 out of 136,655,258

Oryza sativa Japonica Group

Uncovered: 278,641,612 out of 375,049,285
Covered: 96,407,673 out of 375,049,285

Uncovered: 2,740,097 out of 34,403,043
Matches: 24,383,725 out of 34,403,043
Mismatches: 6,365,365 out of 34,403,043
Insertions: 913,856 out of 34,403,043

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

Triticum aestivum Oryza sativa Japonica Group
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}