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Solanum lycopersicum Heinz1706 vs Solanum tuberosum LastZ results

Solanum lycopersicum Heinz1706 (Solanum lycopersicum, SL4.0) and Solanum tuberosum (Solanum tuberosum, SolTub_3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 116. Solanum lycopersicum Heinz1706 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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 lycopersicum Heinz1706Solanum tuberosum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 550,550 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum Heinz1706

Uncovered: 470,439,494 out of 781,672,596
Covered: 311,233,102 out of 781,672,596

Uncovered: 1,720,219 out of 34,561,542
Matches: 30,687,612 out of 34,561,542
Mismatches: 1,999,050 out of 34,561,542
Insertions: 154,661 out of 34,561,542
Identity over aligned base-pairs: 93.4%

Solanum tuberosum

Uncovered: 502,217,642 out of 810,654,046
Covered: 308,436,404 out of 810,654,046

Uncovered: 6,088,236 out of 36,745,425
Matches: 28,533,472 out of 36,745,425
Mismatches: 1,806,732 out of 36,745,425
Insertions: 316,985 out of 36,745,425
Identity over aligned base-pairs: 93.1%

Block size distribution

Size range All 550,550 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10,857
66.5 kb
10 bp - 100 bp
102,722
5.8 Mb
25,002
1.6 Mb
100 bp - 1 kb
306,924
125.8 Mb
55,078
18.9 Mb
1 kb - 10 kb
129,086
272.2 Mb
61,706
172.2 Mb
10 kb - 100 kb
961
21.4 Mb
2,225
52.6 Mb
100 kb - 1 Mb
52
10.2 Mb
1 Mb - 10 Mb
24
87.0 Mb
10 Mb - 100 Mb
6
82.7 Mb