Vitis vinifera vs Triticum aestivum LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 viniferaTriticum aestivum
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 600,712 alignment blocks

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

Uncovered: 445,534,490 out of 486,265,422
Covered: 40,730,932 out of 486,265,422

Uncovered: 9,846,045 out of 32,794,161
Matches: 14,753,946 out of 32,794,161
Mismatches: 7,640,099 out of 32,794,161
Insertions: 554,071 out of 32,794,161
Identity over aligned base-pairs: 64.3%

Triticum aestivum

Uncovered: 14,370,766,009 out of 14,547,261,565
Covered: 176,495,556 out of 14,547,261,565

Uncovered: 52,820,350 out of 133,674,966
Matches: 52,219,646 out of 133,674,966
Mismatches: 26,751,275 out of 133,674,966
Insertions: 1,883,695 out of 133,674,966
Identity over aligned base-pairs: 64.6%

Block size distribution

Size range All 600,712 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,162
15.7 kb
10 bp - 100 bp
103,441
7.3 Mb
43,202
3.1 Mb
100 bp - 1 kb
461,086
143.8 Mb
211,105
75.1 Mb
1 kb - 10 kb
32,917
50.4 Mb
63,795
122.1 Mb
10 kb - 100 kb
106
1.7 Mb
193
2.9 Mb