Vitis vinifera vs Pistacia vera LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Pistacia vera (Pistacia vera, PisVer_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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

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

Chunking parameters

ParameterVitis viniferaPistacia vera
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 368,056 alignment blocks

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

Uncovered: 412,124,048 out of 486,265,422
Covered: 74,141,374 out of 486,265,422

Uncovered: 3,246,138 out of 32,794,161
Matches: 21,441,461 out of 32,794,161
Mismatches: 7,528,243 out of 32,794,161
Insertions: 578,319 out of 32,794,161
Identity over aligned base-pairs: 72.6%

Pistacia vera

Uncovered: 537,566,443 out of 671,152,441
Covered: 133,585,998 out of 671,152,441

Uncovered: 3,083,292 out of 38,113,229
Matches: 25,533,660 out of 38,113,229
Mismatches: 8,885,373 out of 38,113,229
Insertions: 610,904 out of 38,113,229
Identity over aligned base-pairs: 72.9%

Block size distribution

Size range All 368,056 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,582
14.0 kb
10 bp - 100 bp
57,732
3.8 Mb
26,764
1.9 Mb
100 bp - 1 kb
266,233
95.0 Mb
118,955
40.7 Mb
1 kb - 10 kb
41,422
70.1 Mb
38,194
93.5 Mb
10 kb - 100 kb
87
1.6 Mb
1,329
31.9 Mb
100 kb - 1 Mb
19
2.5 Mb