Vitis vinifera vs Ananas comosus LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Ananas comosus (Ananas comosus, F153) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 viniferaAnanas comosus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 173,984 alignment blocks

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

Uncovered: 442,201,882 out of 486,265,422
Covered: 44,063,540 out of 486,265,422

Uncovered: 8,546,873 out of 32,794,161
Matches: 16,190,337 out of 32,794,161
Mismatches: 7,536,067 out of 32,794,161
Insertions: 520,884 out of 32,794,161
Identity over aligned base-pairs: 66.8%

Ananas comosus

Uncovered: 279,533,267 out of 315,839,004
Covered: 36,305,737 out of 315,839,004

Uncovered: 7,262,045 out of 27,915,811
Matches: 13,832,027 out of 27,915,811
Mismatches: 6,358,229 out of 27,915,811
Insertions: 463,510 out of 27,915,811
Identity over aligned base-pairs: 67.0%

Block size distribution

Size range All 173,984 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,165
5.9 kb
10 bp - 100 bp
29,266
2.0 Mb
9,267
656.3 kb
100 bp - 1 kb
134,140
42.4 Mb
47,468
16.9 Mb
1 kb - 10 kb
9,378
14.6 Mb
18,445
40.2 Mb
10 kb - 100 kb
35
626.1 kb
117
1.8 Mb