Vitis vinifera vs Arabidopsis halleri LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 viniferaArabidopsis halleri
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 169,393 alignment blocks

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

Uncovered: 441,514,216 out of 486,265,422
Covered: 44,751,206 out of 486,265,422

Uncovered: 7,610,881 out of 32,794,161
Matches: 16,857,072 out of 32,794,161
Mismatches: 7,695,407 out of 32,794,161
Insertions: 630,801 out of 32,794,161
Identity over aligned base-pairs: 66.9%

Arabidopsis halleri

Uncovered: 156,640,131 out of 196,243,198
Covered: 39,603,067 out of 196,243,198

Uncovered: 12,167,693 out of 38,698,211
Matches: 17,982,649 out of 38,698,211
Mismatches: 8,009,981 out of 38,698,211
Insertions: 537,888 out of 38,698,211
Identity over aligned base-pairs: 67.8%

Block size distribution

Size range All 169,393 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,212
6.5 kb
10 bp - 100 bp
27,525
1.9 Mb
7,357
539.8 kb
100 bp - 1 kb
129,444
42.1 Mb
42,092
15.4 Mb
1 kb - 10 kb
11,177
18.2 Mb
18,290
42.2 Mb
10 kb - 100 kb
35
569.5 kb
281
4.5 Mb
100 kb - 1 Mb
1
103.5 kb