Vitis vinifera vs Phaseolus vulgaris LastZ Results

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Vitis vinifera (Vitis vinifera, IGGP_12x) and Phaseolus vulgaris (Phaseolus vulgaris, PhaVulg1_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: 211,062

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

Uncovered: 428,558,253 out of 486,265,422
Covered: 57,707,169 out of 486,265,422

Uncovered: 5,113,910 out of 32,794,161
Matches: 19,230,055 out of 32,794,161
Mismatches: 7,856,003 out of 32,794,161
Insertions: 594,193 out of 32,794,161

Phaseolus vulgaris

Uncovered: 462,466,362 out of 521,076,696
Covered: 58,610,334 out of 521,076,696

Uncovered: 4,813,619 out of 34,663,348
Matches: 20,978,453 out of 34,663,348
Mismatches: 8,338,417 out of 34,663,348
Insertions: 532,859 out of 34,663,348

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 Phaseolus vulgaris
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}