Vitis vinifera vs Lupinus angustifolius LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) 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: 277,239

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

Uncovered: 429,220,463 out of 486,265,422
Covered: 57,044,959 out of 486,265,422

Uncovered: 5,321,024 out of 32,794,161
Matches: 19,211,179 out of 32,794,161
Mismatches: 7,691,266 out of 32,794,161
Insertions: 570,692 out of 32,794,161

Lupinus angustifolius

Uncovered: 531,619,114 out of 609,203,021
Covered: 77,583,907 out of 609,203,021

Uncovered: 4,582,611 out of 42,631,353
Matches: 27,167,528 out of 42,631,353
Mismatches: 10,194,924 out of 42,631,353
Insertions: 686,290 out of 42,631,353

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 Lupinus angustifolius
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}