Arabidopsis thaliana vs Vitis vinifera BlastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vitis vinifera (Vitis vinifera, IGGP_12x) were aligned using the BlastZ alignment algorithm ( Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9 ) in Ensembl Plants release 76. Arabidopsis thaliana was used as the reference species. After running BlastZ, the raw BlastZ 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: 100,575

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 84,107,370 out of 119,667,750
Covered: 35,560,380 out of 119,667,750

Uncovered: 7,386,566 out of 33,462,323
Matches: 17,874,592 out of 33,462,323
Mismatches: 7,690,735 out of 33,462,323
Insertions: 510,430 out of 33,462,323

Vitis vinifera

Uncovered: 459,810,685 out of 486,265,422
Covered: 26,454,737 out of 486,265,422

Uncovered: 15,149,944 out of 32,794,161
Matches: 12,105,277 out of 32,794,161
Mismatches: 5,087,280 out of 32,794,161
Insertions: 451,660 out of 32,794,161

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)