Vitis vinifera vs Oryza sativa Indica Group LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Oryza sativa Indica Group (Oryza sativa Indica Group, ASM465v1) 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 viniferaOryza sativa Indica Group
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 166,917 alignment blocks

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

Uncovered: 448,981,812 out of 486,265,422
Covered: 37,283,610 out of 486,265,422

Uncovered: 10,668,676 out of 32,794,161
Matches: 14,410,137 out of 32,794,161
Mismatches: 7,243,638 out of 32,794,161
Insertions: 471,710 out of 32,794,161
Identity over aligned base-pairs: 65.1%

Oryza sativa Indica Group

Uncovered: 391,010,596 out of 427,004,890
Covered: 35,994,294 out of 427,004,890

Uncovered: 21,300,848 out of 45,465,969
Matches: 15,671,640 out of 45,465,969
Mismatches: 7,926,603 out of 45,465,969
Insertions: 566,878 out of 45,465,969
Identity over aligned base-pairs: 64.9%

Block size distribution

Size range All 166,917 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,114
5.4 kb
10 bp - 100 bp
27,959
2.0 Mb
7,971
585.0 kb
100 bp - 1 kb
129,773
40.2 Mb
47,142
17.4 Mb
1 kb - 10 kb
8,012
12.7 Mb
17,818
36.4 Mb
10 kb - 100 kb
58
870.2 kb
87
1.4 Mb
100 kb - 1 Mb
1
100.7 kb
1
130.6 kb