Vitis vinifera vs Triticum dicoccoides LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) 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 dicoccoides
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 1,513,583 alignment blocks

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

Uncovered: 445,058,157 out of 486,265,422
Covered: 41,207,265 out of 486,265,422

Uncovered: 10,019,959 out of 32,794,161
Matches: 14,686,726 out of 32,794,161
Mismatches: 7,557,006 out of 32,794,161
Insertions: 530,470 out of 32,794,161
Identity over aligned base-pairs: 64.5%

Triticum dicoccoides

Uncovered: 9,448,585,245 out of 10,079,039,394
Covered: 630,454,149 out of 10,079,039,394

Uncovered: 46,879,058 out of 100,651,268
Matches: 34,727,345 out of 100,651,268
Mismatches: 17,721,530 out of 100,651,268
Insertions: 1,323,335 out of 100,651,268
Identity over aligned base-pairs: 64.6%

Block size distribution

Size range All 1,513,583 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,482
29.2 kb
10 bp - 100 bp
172,773
11.6 Mb
93,461
6.6 Mb
100 bp - 1 kb
1,220,874
490.3 Mb
772,899
351.0 Mb
1 kb - 10 kb
114,399
164.2 Mb
184,934
307.4 Mb
10 kb - 100 kb
55
908.9 kb
129
2.0 Mb