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Arabidopsis thaliana vs Vitis vinifera LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Vitis vinifera (Vitis vinifera, ASM3070453v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 114. 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 126,798 alignment blocks

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

Uncovered: 88,066,539 out of 119,667,750
Covered: 31,601,211 out of 119,667,750

Uncovered: 10,596,223 out of 33,775,569
Matches: 15,856,310 out of 33,775,569
Mismatches: 6,852,063 out of 33,775,569
Insertions: 470,973 out of 33,775,569
Identity over aligned base-pairs: 68.4%

Vitis vinifera

Uncovered: 461,558,452 out of 494,873,210
Covered: 33,314,758 out of 494,873,210

Uncovered: 24,754,888 out of 46,043,106
Matches: 14,392,743 out of 46,043,106
Mismatches: 6,333,536 out of 46,043,106
Insertions: 561,939 out of 46,043,106
Identity over aligned base-pairs: 67.6%

Block size distribution

Size range All 126,798 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,155
6.1 kb
10 bp - 100 bp
19,849
1.4 Mb
4,203
309.7 kb
100 bp - 1 kb
98,144
32.2 Mb
27,186
10.4 Mb
1 kb - 10 kb
7,650
11.4 Mb
13,496
31.0 Mb
10 kb - 100 kb
205
3.2 Mb