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Vitis vinifera vs Triticum aestivum LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 600,712

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 445,534,490 out of 486,265,422
Covered: 40,730,932 out of 486,265,422

Uncovered: 9,846,045 out of 32,794,161
Matches: 14,753,946 out of 32,794,161
Mismatches: 7,640,099 out of 32,794,161
Insertions: 554,071 out of 32,794,161

Triticum aestivum

Uncovered: 14,370,766,009 out of 14,547,261,565
Covered: 176,495,556 out of 14,547,261,565

Uncovered: 52,820,350 out of 133,674,966
Matches: 52,219,646 out of 133,674,966
Mismatches: 26,751,275 out of 133,674,966
Insertions: 1,883,695 out of 133,674,966

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

Vitis vinifera Triticum aestivum
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}