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Solanum lycopersicum vs Lactuca sativa LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Lactuca sativa (Lactuca sativa, Lsat_Salinas_v7) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 105. 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 lycopersicumLactuca sativa
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 273,263 alignment blocks

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

Uncovered: 773,671,984 out of 827,747,456
Covered: 54,075,472 out of 827,747,456

Uncovered: 9,328,857 out of 36,416,191
Matches: 18,379,825 out of 36,416,191
Mismatches: 7,925,695 out of 36,416,191
Insertions: 781,814 out of 36,416,191
Identity over aligned base-pairs: 67.9%

Lactuca sativa

Uncovered: 2,319,716,485 out of 2,391,062,152
Covered: 71,345,667 out of 2,391,062,152

Uncovered: 11,245,935 out of 40,674,853
Matches: 20,105,400 out of 40,674,853
Mismatches: 8,690,462 out of 40,674,853
Insertions: 633,056 out of 40,674,853
Identity over aligned base-pairs: 68.3%

Block size distribution

Size range All 273,263 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,122
11.2 kb
10 bp - 100 bp
45,438
3.1 Mb
16,340
1.2 Mb
100 bp - 1 kb
207,278
67.9 Mb
86,871
31.9 Mb
1 kb - 10 kb
18,377
29.6 Mb
30,935
66.0 Mb
10 kb - 100 kb
46
737.6 kb
163
2.1 Mb
100 kb - 1 Mb
2
260.6 kb
3
448.4 kb