Vigna angularis vs Vigna radiata LastZ Results

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Vigna angularis (Vigna angularis, Vigan1.1) and Vigna radiata (Vigna radiata var. radiata, Vradiata_ver6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vigna angularis 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: 909,780

Genome coverage (bp) Coding exon coverage (bp)
Vigna angularis

Uncovered: 79,751,130 out of 466,744,453
Covered: 386,993,323 out of 466,744,453

Uncovered: 2,014,723 out of 37,822,470
Matches: 31,986,304 out of 37,822,470
Mismatches: 3,514,322 out of 37,822,470
Insertions: 307,121 out of 37,822,470

Vigna radiata var. radiata

Uncovered: 64,915,927 out of 463,085,359
Covered: 398,169,432 out of 463,085,359

Uncovered: 594,912 out of 28,307,530
Matches: 26,418,458 out of 28,307,530
Mismatches: 1,212,698 out of 28,307,530
Insertions: 81,462 out of 28,307,530

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 --matchcount=1000

Chunking parameters

Vigna angularis 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}