Vitis vinifera vs Oryza meridionalis LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) 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 meridionalis
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 146,141 alignment blocks

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

Uncovered: 451,421,947 out of 486,265,422
Covered: 34,843,475 out of 486,265,422

Uncovered: 11,831,463 out of 32,794,161
Matches: 13,661,882 out of 32,794,161
Mismatches: 6,856,756 out of 32,794,161
Insertions: 444,060 out of 32,794,161
Identity over aligned base-pairs: 65.2%

Oryza meridionalis

Uncovered: 305,508,230 out of 335,668,232
Covered: 30,160,002 out of 335,668,232

Uncovered: 15,405,924 out of 35,224,824
Matches: 12,900,968 out of 35,224,824
Mismatches: 6,443,122 out of 35,224,824
Insertions: 474,810 out of 35,224,824
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 146,141 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
943
4.6 kb
10 bp - 100 bp
24,206
1.7 Mb
6,238
460.7 kb
100 bp - 1 kb
113,859
35.4 Mb
39,630
14.7 Mb
1 kb - 10 kb
7,096
11.0 Mb
15,803
32.4 Mb
10 kb - 100 kb
37
609.0 kb
73
1.2 Mb