Vitis vinifera vs Helianthus annuus LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) 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 viniferaHelianthus annuus
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 427,684 alignment blocks

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

Uncovered: 429,487,858 out of 486,265,422
Covered: 56,777,564 out of 486,265,422

Uncovered: 5,868,706 out of 32,794,161
Matches: 18,040,636 out of 32,794,161
Mismatches: 8,109,591 out of 32,794,161
Insertions: 775,228 out of 32,794,161
Identity over aligned base-pairs: 67.0%

Helianthus annuus

Uncovered: 2,902,182,699 out of 3,027,844,945
Covered: 125,662,246 out of 3,027,844,945

Uncovered: 12,509,694 out of 54,343,734
Matches: 28,704,360 out of 54,343,734
Mismatches: 12,374,279 out of 54,343,734
Insertions: 755,401 out of 54,343,734
Identity over aligned base-pairs: 68.6%

Block size distribution

Size range All 427,684 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,527
13.0 kb
10 bp - 100 bp
73,261
5.1 Mb
32,031
2.3 Mb
100 bp - 1 kb
323,919
104.2 Mb
153,424
53.6 Mb
1 kb - 10 kb
27,641
45.7 Mb
44,995
96.5 Mb
10 kb - 100 kb
336
4.5 Mb
471
7.1 Mb