Vitis vinifera vs Oryza brachyantha LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Oryza brachyantha (Oryza brachyantha, Oryza_brachyantha.v1.4b) 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 brachyantha
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 149,462 alignment blocks

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

Uncovered: 450,338,649 out of 486,265,422
Covered: 35,926,773 out of 486,265,422

Uncovered: 11,168,333 out of 32,794,161
Matches: 13,922,074 out of 32,794,161
Mismatches: 7,257,306 out of 32,794,161
Insertions: 446,448 out of 32,794,161
Identity over aligned base-pairs: 64.4%

Oryza brachyantha

Uncovered: 230,055,725 out of 260,838,168
Covered: 30,782,443 out of 260,838,168

Uncovered: 12,859,417 out of 33,473,466
Matches: 13,445,422 out of 33,473,466
Mismatches: 6,749,793 out of 33,473,466
Insertions: 418,834 out of 33,473,466
Identity over aligned base-pairs: 65.2%

Block size distribution

Size range All 149,462 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
962
4.7 kb
10 bp - 100 bp
25,393
1.8 Mb
6,649
490.0 kb
100 bp - 1 kb
116,043
35.7 Mb
40,327
14.9 Mb
1 kb - 10 kb
7,029
11.4 Mb
15,865
32.7 Mb
10 kb - 100 kb
35
545.3 kb
85
1.4 Mb