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Vitis vinifera vs Citrus clementina LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Citrus clementina (Citrus clementina, Citrus_clementina_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: 226,039

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

Uncovered: 416,768,149 out of 486,265,422
Covered: 69,497,273 out of 486,265,422

Uncovered: 3,623,915 out of 32,794,161
Matches: 21,071,346 out of 32,794,161
Mismatches: 7,587,186 out of 32,794,161
Insertions: 511,714 out of 32,794,161

Citrus clementina

Uncovered: 231,722,432 out of 301,364,702
Covered: 69,642,270 out of 301,364,702

Uncovered: 2,716,678 out of 30,721,724
Matches: 20,086,813 out of 30,721,724
Mismatches: 7,359,375 out of 30,721,724
Insertions: 558,858 out of 30,721,724

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 Citrus clementina
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}