Vitis vinifera vs Oryza nivara LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Oryza nivara (Oryza sativa f. spontanea, Oryza_nivara_v1.0) 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 nivara
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 156,601 alignment blocks

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

Uncovered: 450,615,771 out of 486,265,422
Covered: 35,649,651 out of 486,265,422

Uncovered: 10,942,452 out of 32,794,161
Matches: 14,290,845 out of 32,794,161
Mismatches: 7,093,969 out of 32,794,161
Insertions: 466,895 out of 32,794,161
Identity over aligned base-pairs: 65.4%

Oryza nivara

Uncovered: 304,898,129 out of 337,950,324
Covered: 33,052,195 out of 337,950,324

Uncovered: 19,363,048 out of 42,562,444
Matches: 15,080,332 out of 42,562,444
Mismatches: 7,561,567 out of 42,562,444
Insertions: 557,497 out of 42,562,444
Identity over aligned base-pairs: 65.0%

Block size distribution

Size range All 156,601 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,050
5.1 kb
10 bp - 100 bp
26,080
1.8 Mb
6,932
511.7 kb
100 bp - 1 kb
121,918
37.9 Mb
42,070
15.5 Mb
1 kb - 10 kb
7,525
11.4 Mb
16,958
34.5 Mb
10 kb - 100 kb
28
514.8 kb
58
1.0 Mb