Vitis vinifera vs Arabidopsis lyrata LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 66. Vitis vinifera was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Statistics over 132,631 alignment blocks

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

Uncovered: 439,074,194 out of 486,265,422
Covered: 47,191,228 out of 486,265,422

Uncovered: 6,979,177 out of 32,794,161
Matches: 17,477,875 out of 32,794,161
Mismatches: 7,718,228 out of 32,794,161
Insertions: 618,881 out of 32,794,161
Identity over aligned base-pairs: 67.7%

Arabidopsis lyrata

Uncovered: 179,984,924 out of 206,667,935
Covered: 26,683,011 out of 206,667,935

Uncovered: 17,206,046 out of 35,389,059
Matches: 12,512,430 out of 35,389,059
Mismatches: 5,299,680 out of 35,389,059
Insertions: 370,903 out of 35,389,059
Identity over aligned base-pairs: 68.8%