Vitis vinifera vs Ipomoea triloba LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 viniferaIpomoea triloba
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 229,316 alignment blocks

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

Uncovered: 430,938,265 out of 486,265,422
Covered: 55,327,157 out of 486,265,422

Uncovered: 5,156,138 out of 32,794,161
Matches: 19,078,239 out of 32,794,161
Mismatches: 7,977,415 out of 32,794,161
Insertions: 582,369 out of 32,794,161
Identity over aligned base-pairs: 69.0%

Ipomoea triloba

Uncovered: 400,114,995 out of 461,827,428
Covered: 61,712,433 out of 461,827,428

Uncovered: 6,960,581 out of 39,533,495
Matches: 22,641,572 out of 39,533,495
Mismatches: 9,263,319 out of 39,533,495
Insertions: 668,023 out of 39,533,495
Identity over aligned base-pairs: 69.5%

Block size distribution

Size range All 229,316 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,722
8.8 kb
10 bp - 100 bp
37,887
2.6 Mb
12,927
930.3 kb
100 bp - 1 kb
173,046
57.7 Mb
61,624
21.6 Mb
1 kb - 10 kb
16,575
26.6 Mb
22,128
52.5 Mb
10 kb - 100 kb
86
2.0 Mb
577
11.9 Mb
100 kb - 1 Mb
10
2.0 Mb