Vitis vinifera vs Prunus persica LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Prunus persica (Prunus persica, Prunus_persica_NCBIv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 viniferaPrunus persica
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 203,095 alignment blocks

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

Uncovered: 421,423,085 out of 486,265,422
Covered: 64,842,337 out of 486,265,422

Uncovered: 3,562,734 out of 32,794,161
Matches: 21,321,593 out of 32,794,161
Mismatches: 7,413,599 out of 32,794,161
Insertions: 496,235 out of 32,794,161
Identity over aligned base-pairs: 72.9%

Prunus persica

Uncovered: 171,058,246 out of 227,411,381
Covered: 56,353,135 out of 227,411,381

Uncovered: 3,927,321 out of 33,236,255
Matches: 21,161,000 out of 33,236,255
Mismatches: 7,514,872 out of 33,236,255
Insertions: 633,062 out of 33,236,255
Identity over aligned base-pairs: 72.2%

Block size distribution

Size range All 203,095 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,596
8.9 kb
10 bp - 100 bp
34,795
2.3 Mb
12,892
930.9 kb
100 bp - 1 kb
148,139
51.1 Mb
53,376
17.6 Mb
1 kb - 10 kb
18,527
30.7 Mb
14,070
33.6 Mb
10 kb - 100 kb
38
775.3 kb
400
9.7 Mb
100 kb - 1 Mb
60
22.0 Mb
1 Mb - 10 Mb
1
1.1 Mb