Vitis vinifera vs Vigna radiata LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) 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: 267,561

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

Uncovered: 423,655,145 out of 486,265,422
Covered: 62,610,277 out of 486,265,422

Uncovered: 4,926,852 out of 32,794,161
Matches: 19,265,117 out of 32,794,161
Mismatches: 8,002,694 out of 32,794,161
Insertions: 599,498 out of 32,794,161

Vigna radiata var. radiata

Uncovered: 386,532,285 out of 463,085,359
Covered: 76,553,074 out of 463,085,359

Uncovered: 4,928,407 out of 36,130,572
Matches: 21,740,915 out of 36,130,572
Mismatches: 8,871,982 out of 36,130,572
Insertions: 589,268 out of 36,130,572

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 Vigna radiata
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}