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Arabidopsis thaliana vs Vitis vinifera LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vitis vinifera (Vitis vinifera, PN40024.v4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. Arabidopsis thaliana 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

ParameterArabidopsis thalianaVitis vinifera
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 127,902 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 87,996,239 out of 119,667,750
Covered: 31,671,511 out of 119,667,750

Uncovered: 10,555,439 out of 33,775,569
Matches: 15,883,465 out of 33,775,569
Mismatches: 6,862,744 out of 33,775,569
Insertions: 473,921 out of 33,775,569
Identity over aligned base-pairs: 68.4%

Vitis vinifera

Uncovered: 441,990,524 out of 475,604,073
Covered: 33,613,549 out of 475,604,073

Uncovered: 15,664,505 out of 37,909,762
Matches: 15,038,381 out of 37,909,762
Mismatches: 6,627,721 out of 37,909,762
Insertions: 579,155 out of 37,909,762
Identity over aligned base-pairs: 67.6%

Block size distribution

Size range All 127,902 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,192
6.3 kb
10 bp - 100 bp
20,104
1.4 Mb
4,411
324.6 kb
100 bp - 1 kb
98,957
32.5 Mb
27,389
10.4 Mb
1 kb - 10 kb
7,649
11.4 Mb
13,625
31.2 Mb
10 kb - 100 kb
208
3.3 Mb