Vitis vinifera vs Aegilops tauschii LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) 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: 249,685

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

Uncovered: 448,899,562 out of 486,265,422
Covered: 37,365,860 out of 486,265,422

Uncovered: 10,596,954 out of 32,794,161
Matches: 14,413,818 out of 32,794,161
Mismatches: 7,297,683 out of 32,794,161
Insertions: 485,706 out of 32,794,161

Aegilops tauschii subsp. strangulata

Uncovered: 4,162,071,900 out of 4,224,915,394
Covered: 62,843,494 out of 4,224,915,394

Uncovered: 23,986,931 out of 53,210,770
Matches: 18,785,597 out of 53,210,770
Mismatches: 9,662,675 out of 53,210,770
Insertions: 775,567 out of 53,210,770

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 Aegilops tauschii
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}