Vitis vinifera vs Ananas comosus LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Ananas comosus (Ananas comosus, F153) 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: 173,984

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

Uncovered: 442,201,882 out of 486,265,422
Covered: 44,063,540 out of 486,265,422

Uncovered: 8,546,873 out of 32,794,161
Matches: 16,190,337 out of 32,794,161
Mismatches: 7,536,067 out of 32,794,161
Insertions: 520,884 out of 32,794,161

Ananas comosus

Uncovered: 279,533,267 out of 315,839,004
Covered: 36,305,737 out of 315,839,004

Uncovered: 7,262,045 out of 27,915,811
Matches: 13,832,027 out of 27,915,811
Mismatches: 6,358,229 out of 27,915,811
Insertions: 463,510 out of 27,915,811

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 Ananas comosus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options