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Solanum lycopersicum vs Actinidia chinensis LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Actinidia chinensis (Actinidia chinensis var. chinensis, Red5_PS1_1.69.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 96. 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 lycopersicumActinidia chinensis
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 168,215 alignment blocks

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

Uncovered: 766,948,284 out of 827,747,456
Covered: 60,799,172 out of 827,747,456

Uncovered: 7,417,761 out of 36,416,191
Matches: 20,409,975 out of 36,416,191
Mismatches: 8,041,300 out of 36,416,191
Insertions: 547,155 out of 36,416,191
Identity over aligned base-pairs: 70.4%

Actinidia chinensis

Uncovered: 513,238,456 out of 553,842,477
Covered: 40,604,021 out of 553,842,477

Uncovered: 20,842,706 out of 42,227,027
Matches: 15,146,151 out of 42,227,027
Mismatches: 5,789,225 out of 42,227,027
Insertions: 448,945 out of 42,227,027
Identity over aligned base-pairs: 70.8%

Block size distribution

Size range All 168,215 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,671
7.9 kb
10 bp - 100 bp
27,250
1.8 Mb
11,202
789.5 kb
100 bp - 1 kb
127,251
42.6 Mb
41,929
14.5 Mb
1 kb - 10 kb
12,032
20.0 Mb
15,606
37.5 Mb
10 kb - 100 kb
11
143.3 kb
413
8.8 Mb
100 kb - 1 Mb
14
2.9 Mb