Vitis vinifera vs Oryza sativa Japonica Group LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. 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 98,467 alignment blocks

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

Uncovered: 464,990,539 out of 486,265,422
Covered: 21,274,883 out of 486,265,422

Uncovered: 18,087,787 out of 32,794,161
Matches: 9,763,986 out of 32,794,161
Mismatches: 4,624,253 out of 32,794,161
Insertions: 318,135 out of 32,794,161
Identity over aligned base-pairs: 66.4%

Oryza sativa Japonica Group

Uncovered: 342,513,518 out of 374,424,240
Covered: 31,910,722 out of 374,424,240

Uncovered: 14,082,220 out of 34,124,807
Matches: 13,210,158 out of 34,124,807
Mismatches: 6,381,475 out of 34,124,807
Insertions: 450,954 out of 34,124,807
Identity over aligned base-pairs: 65.9%