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Solanum lycopersicum vs Helianthus annuus LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Helianthus annuus (Helianthus annuus, HanXRQr2.0-SUNRISE) 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 lycopersicumHelianthus annuus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 320,158 alignment blocks

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

Uncovered: 774,215,512 out of 827,747,456
Covered: 53,531,944 out of 827,747,456

Uncovered: 9,394,229 out of 36,416,191
Matches: 18,287,914 out of 36,416,191
Mismatches: 7,946,351 out of 36,416,191
Insertions: 787,697 out of 36,416,191
Identity over aligned base-pairs: 67.7%

Helianthus annuus

Uncovered: 2,925,120,324 out of 3,009,595,538
Covered: 84,475,214 out of 3,009,595,538

Uncovered: 25,767,059 out of 64,710,370
Matches: 26,513,306 out of 64,710,370
Mismatches: 11,664,042 out of 64,710,370
Insertions: 765,963 out of 64,710,370
Identity over aligned base-pairs: 68.1%

Block size distribution

Size range All 320,158 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,557
12.8 kb
10 bp - 100 bp
54,330
3.7 Mb
20,296
1.5 Mb
100 bp - 1 kb
243,418
77.7 Mb
101,946
36.2 Mb
1 kb - 10 kb
19,798
32.5 Mb
35,738
75.1 Mb
10 kb - 100 kb
55
857.6 kb
137
1.9 Mb
100 kb - 1 Mb
1
131.7 kb