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Solanum lycopersicum vs Capsicum annuum LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Capsicum annuum (Capsicum annuum, ASM51225v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 lycopersicumCapsicum annuum
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 782,928 alignment blocks

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

Uncovered: 653,364,965 out of 827,747,456
Covered: 174,382,491 out of 827,747,456

Uncovered: 5,906,138 out of 36,416,191
Matches: 26,454,733 out of 36,416,191
Mismatches: 3,692,161 out of 36,416,191
Insertions: 363,159 out of 36,416,191
Identity over aligned base-pairs: 86.7%

Capsicum annuum

Uncovered: 2,548,778,207 out of 3,063,864,880
Covered: 515,086,673 out of 3,063,864,880

Uncovered: 7,250,930 out of 39,113,865
Matches: 27,423,690 out of 39,113,865
Mismatches: 3,995,841 out of 39,113,865
Insertions: 443,404 out of 39,113,865
Identity over aligned base-pairs: 86.1%

Block size distribution

Size range All 782,928 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10,409
60.4 kb
10 bp - 100 bp
107,153
6.3 Mb
35,767
2.4 Mb
100 bp - 1 kb
476,865
193.7 Mb
135,907
45.5 Mb
1 kb - 10 kb
187,833
383.4 Mb
131,699
414.5 Mb
10 kb - 100 kb
656
15.9 Mb
3,916
75.0 Mb
100 kb - 1 Mb
12
1.3 Mb
175
39.5 Mb
1 Mb - 10 Mb
9
23.7 Mb