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Solanum lycopersicum vs Ipomoea triloba LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Ipomoea triloba (Ipomoea triloba, ASM357664v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 lycopersicumIpomoea triloba
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 249,773 alignment blocks

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

Uncovered: 759,433,395 out of 827,747,456
Covered: 68,314,061 out of 827,747,456

Uncovered: 6,660,989 out of 36,416,191
Matches: 21,375,571 out of 36,416,191
Mismatches: 7,802,112 out of 36,416,191
Insertions: 577,519 out of 36,416,191
Identity over aligned base-pairs: 71.8%

Ipomoea triloba

Uncovered: 387,616,713 out of 461,827,428
Covered: 74,210,715 out of 461,827,428

Uncovered: 5,543,317 out of 39,533,495
Matches: 24,321,750 out of 39,533,495
Mismatches: 8,937,967 out of 39,533,495
Insertions: 730,461 out of 39,533,495
Identity over aligned base-pairs: 71.6%

Block size distribution

Size range All 249,773 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,977
10.3 kb
10 bp - 100 bp
38,762
2.5 Mb
16,199
1.1 Mb
100 bp - 1 kb
185,547
65.1 Mb
63,884
22.4 Mb
1 kb - 10 kb
23,342
39.1 Mb
25,449
62.0 Mb
10 kb - 100 kb
143
3.0 Mb
806
17.0 Mb
100 kb - 1 Mb
2
204.5 kb
32
7.5 Mb