Vitis vinifera vs Triticum dicoccoides LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) 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: 1,513,583

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

Uncovered: 445,058,157 out of 486,265,422
Covered: 41,207,265 out of 486,265,422

Uncovered: 10,019,959 out of 32,794,161
Matches: 14,686,726 out of 32,794,161
Mismatches: 7,557,006 out of 32,794,161
Insertions: 530,470 out of 32,794,161

Triticum dicoccoides

Uncovered: 9,448,585,245 out of 10,079,039,394
Covered: 630,454,149 out of 10,079,039,394

Uncovered: 46,879,058 out of 100,651,268
Matches: 34,727,345 out of 100,651,268
Mismatches: 17,721,530 out of 100,651,268
Insertions: 1,323,335 out of 100,651,268

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 dicoccoides
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}