Vitis vinifera vs Physcomitrella patens LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Physcomitrella patens (Physcomitrella patens, Phypa_V3) 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: 122,081

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

Uncovered: 465,402,238 out of 486,265,422
Covered: 20,863,184 out of 486,265,422

Uncovered: 19,139,628 out of 32,794,161
Matches: 8,696,779 out of 32,794,161
Mismatches: 4,712,561 out of 32,794,161
Insertions: 245,193 out of 32,794,161

Physcomitrella patens

Uncovered: 452,970,698 out of 471,852,792
Covered: 18,882,094 out of 471,852,792

Uncovered: 21,053,048 out of 34,318,961
Matches: 8,570,803 out of 34,318,961
Mismatches: 4,424,362 out of 34,318,961
Insertions: 270,748 out of 34,318,961

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Physcomitrella patens
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}