Vitis vinifera vs Triticum urartu LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Triticum urartu (Triticum urartu, ASM34745v1) 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 urartu
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 215,140 alignment blocks

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

Uncovered: 448,877,076 out of 486,265,422
Covered: 37,388,346 out of 486,265,422

Uncovered: 11,918,239 out of 32,794,161
Matches: 13,064,460 out of 32,794,161
Mismatches: 7,376,376 out of 32,794,161
Insertions: 435,086 out of 32,794,161
Identity over aligned base-pairs: 62.6%

Triticum urartu

Uncovered: 3,695,816,329 out of 3,747,163,292
Covered: 51,346,963 out of 3,747,163,292

Uncovered: 15,993,433 out of 36,194,921
Matches: 13,115,191 out of 36,194,921
Mismatches: 6,654,278 out of 36,194,921
Insertions: 432,019 out of 36,194,921
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 215,140 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,124
5.6 kb
10 bp - 100 bp
39,230
2.8 Mb
15,600
1.1 Mb
100 bp - 1 kb
163,444
50.6 Mb
77,102
27.7 Mb
1 kb - 10 kb
11,277
18.4 Mb
21,733
42.1 Mb
10 kb - 100 kb
65
996.5 kb
111
1.8 Mb