Solanum lycopersicum vs Helianthus annuus LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 size10,100,00010,100,000
Overlap100,000100,000
Group set size10,100,00010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 463,312 alignment blocks

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

Uncovered: 763,183,339 out of 827,747,456
Covered: 64,564,117 out of 827,747,456

Uncovered: 8,659,175 out of 35,932,555
Matches: 18,237,324 out of 35,932,555
Mismatches: 8,242,284 out of 35,932,555
Insertions: 793,772 out of 35,932,555
Identity over aligned base-pairs: 66.9%

Helianthus annuus

Uncovered: 2,875,648,807 out of 3,027,844,945
Covered: 152,196,138 out of 3,027,844,945

Uncovered: 13,046,464 out of 54,343,734
Matches: 28,155,573 out of 54,343,734
Mismatches: 12,328,200 out of 54,343,734
Insertions: 813,497 out of 54,343,734
Identity over aligned base-pairs: 68.2%

Block size distribution

Size range All 463,312 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,665
13.6 kb
10 bp - 100 bp
81,255
5.6 Mb
41,507
2.9 Mb
100 bp - 1 kb
341,998
114.8 Mb
161,160
57.0 Mb
1 kb - 10 kb
36,962
68.0 Mb
56,804
124.9 Mb
10 kb - 100 kb
429
5.1 Mb
593
8.5 Mb
100 kb - 1 Mb
3
311.3 kb
3
444.9 kb