Vitis vinifera vs Saccharum spontaneum LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Saccharum spontaneum (Saccharum spontaneum, Sspon.HiC_chr_asm) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 viniferaSaccharum spontaneum
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 594,172 alignment blocks

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

Uncovered: 447,014,651 out of 486,265,422
Covered: 39,250,771 out of 486,265,422

Uncovered: 10,104,150 out of 32,794,161
Matches: 14,740,017 out of 32,794,161
Mismatches: 7,422,332 out of 32,794,161
Insertions: 527,662 out of 32,794,161
Identity over aligned base-pairs: 65.0%

Saccharum spontaneum

Uncovered: 2,729,909,429 out of 2,900,240,836
Covered: 170,331,407 out of 2,900,240,836

Uncovered: 23,241,196 out of 62,027,027
Matches: 25,430,375 out of 62,027,027
Mismatches: 12,477,803 out of 62,027,027
Insertions: 877,653 out of 62,027,027
Identity over aligned base-pairs: 65.6%

Block size distribution

Size range All 594,172 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,581
17.1 kb
10 bp - 100 bp
96,190
6.8 Mb
30,389
2.2 Mb
100 bp - 1 kb
464,971
145.2 Mb
174,394
64.7 Mb
1 kb - 10 kb
29,375
43.9 Mb
66,802
128.0 Mb
10 kb - 100 kb
55
996.3 kb
122
1.9 Mb
100 kb - 1 Mb
1
100.1 kb