Vitis vinifera vs Vigna angularis LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Vigna angularis (Vigna angularis, Vigan1.1) 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: 240,599

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

Uncovered: 419,051,022 out of 486,265,422
Covered: 67,214,400 out of 486,265,422

Uncovered: 4,781,089 out of 32,794,161
Matches: 19,601,592 out of 32,794,161
Mismatches: 7,811,602 out of 32,794,161
Insertions: 599,878 out of 32,794,161

Vigna angularis

Uncovered: 409,063,313 out of 466,744,453
Covered: 57,681,140 out of 466,744,453

Uncovered: 10,117,769 out of 37,822,470
Matches: 19,611,734 out of 37,822,470
Mismatches: 7,600,565 out of 37,822,470
Insertions: 492,402 out of 37,822,470

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Vigna angularis
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}