Vitis vinifera vs Daucus carota LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Daucus carota (Daucus carota subsp. sativus, ASM162521v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 viniferaDaucus carota
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 267,439 alignment blocks

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

Uncovered: 415,634,217 out of 486,265,422
Covered: 70,631,205 out of 486,265,422

Uncovered: 4,901,141 out of 32,794,161
Matches: 19,463,253 out of 32,794,161
Mismatches: 7,839,216 out of 32,794,161
Insertions: 590,551 out of 32,794,161
Identity over aligned base-pairs: 69.8%

Daucus carota

Uncovered: 355,089,636 out of 421,502,825
Covered: 66,413,189 out of 421,502,825

Uncovered: 7,791,399 out of 38,118,360
Matches: 21,343,590 out of 38,118,360
Mismatches: 8,440,213 out of 38,118,360
Insertions: 543,158 out of 38,118,360
Identity over aligned base-pairs: 70.4%

Block size distribution

Size range All 267,439 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,940
9.9 kb
10 bp - 100 bp
43,651
2.9 Mb
17,840
1.2 Mb
100 bp - 1 kb
197,431
67.3 Mb
76,941
26.7 Mb
1 kb - 10 kb
24,417
39.8 Mb
29,998
71.9 Mb
10 kb - 100 kb
543
10.0 Mb
100 kb - 1 Mb
1
123.1 kb