Vitis vinifera vs Olea europaea var. sylvestris LastZ results

Vitis vinifera (Vitis vinifera, 12X) and Olea europaea var. sylvestris (Olea europaea var. sylvestris, O_europaea_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 viniferaOlea europaea var. sylvestris
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 385,083 alignment blocks

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

Uncovered: 401,264,704 out of 486,265,422
Covered: 85,000,718 out of 486,265,422

Uncovered: 4,571,948 out of 32,794,161
Matches: 18,958,357 out of 32,794,161
Mismatches: 8,683,146 out of 32,794,161
Insertions: 580,710 out of 32,794,161
Identity over aligned base-pairs: 67.2%

Olea europaea var. sylvestris

Uncovered: 1,011,634,654 out of 1,140,989,389
Covered: 129,354,735 out of 1,140,989,389

Uncovered: 16,177,953 out of 52,755,300
Matches: 25,782,808 out of 52,755,300
Mismatches: 10,124,931 out of 52,755,300
Insertions: 669,608 out of 52,755,300
Identity over aligned base-pairs: 70.5%

Block size distribution

Size range All 385,083 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,408
12.7 kb
10 bp - 100 bp
64,759
4.4 Mb
33,827
2.4 Mb
100 bp - 1 kb
279,132
94.1 Mb
131,881
45.3 Mb
1 kb - 10 kb
38,352
77.6 Mb
45,886
117.6 Mb
10 kb - 100 kb
432
6.7 Mb
1,119
17.4 Mb