Vitis vinifera vs Oryza rufipogon LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Oryza rufipogon (Oryza rufipogon, OR_W1943) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 viniferaOryza rufipogon
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 158,847 alignment blocks

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

Uncovered: 450,815,479 out of 486,265,422
Covered: 35,449,943 out of 486,265,422

Uncovered: 10,889,619 out of 32,794,161
Matches: 14,329,525 out of 32,794,161
Mismatches: 7,107,494 out of 32,794,161
Insertions: 467,523 out of 32,794,161
Identity over aligned base-pairs: 65.4%

Oryza rufipogon

Uncovered: 304,995,270 out of 338,040,714
Covered: 33,045,444 out of 338,040,714

Uncovered: 19,580,905 out of 42,763,723
Matches: 15,066,003 out of 42,763,723
Mismatches: 7,564,000 out of 42,763,723
Insertions: 552,815 out of 42,763,723
Identity over aligned base-pairs: 65.0%

Block size distribution

Size range All 158,847 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,078
5.4 kb
10 bp - 100 bp
26,692
1.9 Mb
7,287
538.4 kb
100 bp - 1 kb
123,805
38.3 Mb
43,222
15.8 Mb
1 kb - 10 kb
7,255
10.8 Mb
16,840
34.2 Mb
10 kb - 100 kb
17
341.1 kb
47
823.5 kb