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Oryza sativa Japonica Group vs Solanum lycopersicum LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Solanum lycopersicum (Solanum lycopersicum, SL3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Oryza sativa Japonica Group 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

ParameterOryza sativa Japonica GroupSolanum lycopersicum
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 140,336 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 344,760,716 out of 375,049,285
Covered: 30,288,569 out of 375,049,285

Uncovered: 15,781,338 out of 34,403,043
Matches: 11,965,326 out of 34,403,043
Mismatches: 6,262,874 out of 34,403,043
Insertions: 393,505 out of 34,403,043
Identity over aligned base-pairs: 64.3%

Solanum lycopersicum

Uncovered: 796,901,535 out of 827,747,456
Covered: 30,845,921 out of 827,747,456

Uncovered: 15,582,487 out of 35,932,555
Matches: 13,231,972 out of 35,932,555
Mismatches: 6,743,906 out of 35,932,555
Insertions: 374,190 out of 35,932,555
Identity over aligned base-pairs: 65.0%

Block size distribution

Size range All 140,336 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
992
4.9 kb
10 bp - 100 bp
23,479
1.7 Mb
6,373
462.0 kb
100 bp - 1 kb
109,230
33.8 Mb
33,509
12.8 Mb
1 kb - 10 kb
6,634
9.9 Mb
15,526
31.7 Mb
10 kb - 100 kb
1
10.8 kb
33
432.3 kb