Solanum lycopersicum vs Olea europaea var. sylvestris LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) 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. Solanum lycopersicum 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

ParameterSolanum lycopersicumOlea europaea var. sylvestris
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 389,617 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum

Uncovered: 735,893,467 out of 827,747,456
Covered: 91,853,989 out of 827,747,456

Uncovered: 6,772,168 out of 36,416,191
Matches: 19,987,942 out of 36,416,191
Mismatches: 9,046,134 out of 36,416,191
Insertions: 609,947 out of 36,416,191
Identity over aligned base-pairs: 67.4%

Olea europaea var. sylvestris

Uncovered: 1,004,259,077 out of 1,140,989,389
Covered: 136,730,312 out of 1,140,989,389

Uncovered: 15,760,929 out of 52,755,300
Matches: 26,046,053 out of 52,755,300
Mismatches: 10,156,338 out of 52,755,300
Insertions: 791,980 out of 52,755,300
Identity over aligned base-pairs: 70.4%

Block size distribution

Size range All 389,617 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,556
13.3 kb
10 bp - 100 bp
67,052
4.5 Mb
37,521
2.6 Mb
100 bp - 1 kb
278,126
95.6 Mb
125,322
43.9 Mb
1 kb - 10 kb
41,422
88.7 Mb
49,723
130.4 Mb
10 kb - 100 kb
456
6.6 Mb
1,199
18.4 Mb
100 kb - 1 Mb
5
613.9 kb
6
735.1 kb