Vitis vinifera vs Populus trichocarpa LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 viniferaPopulus trichocarpa
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 273,966 alignment blocks

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

Uncovered: 408,421,153 out of 486,265,422
Covered: 77,844,269 out of 486,265,422

Uncovered: 3,260,348 out of 32,794,161
Matches: 21,431,867 out of 32,794,161
Mismatches: 7,557,876 out of 32,794,161
Insertions: 544,070 out of 32,794,161
Identity over aligned base-pairs: 72.6%

Populus trichocarpa

Uncovered: 353,459,398 out of 434,132,815
Covered: 80,673,417 out of 434,132,815

Uncovered: 5,831,070 out of 48,383,886
Matches: 30,880,427 out of 48,383,886
Mismatches: 10,826,839 out of 48,383,886
Insertions: 845,550 out of 48,383,886
Identity over aligned base-pairs: 72.6%

Block size distribution

Size range All 273,966 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,115
11.1 kb
10 bp - 100 bp
42,561
2.8 Mb
14,710
1.1 Mb
100 bp - 1 kb
200,406
72.0 Mb
68,150
23.8 Mb
1 kb - 10 kb
28,884
48.0 Mb
22,254
54.5 Mb
10 kb - 100 kb
807
20.6 Mb
100 kb - 1 Mb
93
21.7 Mb
1 Mb - 10 Mb
1
1.2 Mb