Vitis vinifera vs Solanum lycopersicum LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Solanum lycopersicum (Solanum lycopersicum, SL3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 viniferaSolanum lycopersicum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 214,156 alignment blocks

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

Uncovered: 431,437,399 out of 486,265,422
Covered: 54,828,023 out of 486,265,422

Uncovered: 5,279,344 out of 32,794,161
Matches: 19,022,420 out of 32,794,161
Mismatches: 7,923,963 out of 32,794,161
Insertions: 568,434 out of 32,794,161
Identity over aligned base-pairs: 69.1%

Solanum lycopersicum

Uncovered: 774,782,364 out of 827,747,456
Covered: 52,965,092 out of 827,747,456

Uncovered: 7,625,820 out of 35,932,555
Matches: 19,736,949 out of 35,932,555
Mismatches: 8,064,781 out of 35,932,555
Insertions: 505,005 out of 35,932,555
Identity over aligned base-pairs: 69.7%

Block size distribution

Size range All 214,156 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,477
7.7 kb
10 bp - 100 bp
36,610
2.5 Mb
14,545
1.1 Mb
100 bp - 1 kb
161,236
52.4 Mb
62,454
21.2 Mb
1 kb - 10 kb
14,781
23.8 Mb
19,123
44.1 Mb
10 kb - 100 kb
50
983.8 kb
408
9.1 Mb
100 kb - 1 Mb
2
247.2 kb
21
4.6 Mb