Arabidopsis thaliana vs Vitis vinifera LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vitis vinifera (Vitis vinifera, 12X) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 90. 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 size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 157,480 alignment blocks

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

Uncovered: 84,605,119 out of 119,667,750
Covered: 35,062,631 out of 119,667,750

Uncovered: 8,073,411 out of 33,775,569
Matches: 17,538,889 out of 33,775,569
Mismatches: 7,629,060 out of 33,775,569
Insertions: 534,209 out of 33,775,569
Identity over aligned base-pairs: 68.2%

Vitis vinifera

Uncovered: 444,212,636 out of 486,265,422
Covered: 42,052,786 out of 486,265,422

Uncovered: 7,863,123 out of 32,794,161
Matches: 16,837,656 out of 32,794,161
Mismatches: 7,471,837 out of 32,794,161
Insertions: 621,545 out of 32,794,161
Identity over aligned base-pairs: 67.5%

Block size distribution

Size range All 157,480 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,181
6.4 kb
10 bp - 100 bp
25,946
1.8 Mb
6,927
501.4 kb
100 bp - 1 kb
120,459
39.2 Mb
37,620
13.7 Mb
1 kb - 10 kb
9,894
14.9 Mb
16,306
37.6 Mb
10 kb - 100 kb
254
4.1 Mb
100 kb - 1 Mb
1
104.2 kb