In this section

Vigna angularis vs Vigna radiata LastZ results

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 95. Vigna angularis was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterVigna angularisVigna radiata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 909,780 alignment blocks

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
Identity over aligned base-pairs: 89.3%

Vigna 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
Identity over aligned base-pairs: 95.3%

Block size distribution

Size range All 909,780 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16,284
85.3 kb
10 bp - 100 bp
153,036
8.9 Mb
40,150
2.7 Mb
100 bp - 1 kb
571,232
219.0 Mb
182,655
68.8 Mb
1 kb - 10 kb
168,552
355.9 Mb
92,882
237.5 Mb
10 kb - 100 kb
676
8.9 Mb
4,141
89.6 Mb
100 kb - 1 Mb
353
88.6 Mb
1 Mb - 10 Mb
27
93.8 Mb
10 Mb - 100 Mb
1
11.7 Mb