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Solanum lycopersicum vs Coffea canephora LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Coffea canephora (Coffea canephora str. DH200-94, AUK_PRJEB4211_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 lycopersicumCoffea canephora
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 219,875 alignment blocks

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

Uncovered: 739,264,936 out of 827,747,456
Covered: 88,482,520 out of 827,747,456

Uncovered: 6,901,767 out of 36,416,191
Matches: 20,768,261 out of 36,416,191
Mismatches: 8,279,684 out of 36,416,191
Insertions: 466,479 out of 36,416,191
Identity over aligned base-pairs: 70.4%

Coffea canephora

Uncovered: 501,879,159 out of 568,611,505
Covered: 66,732,346 out of 568,611,505

Uncovered: 3,987,211 out of 30,830,841
Matches: 18,755,824 out of 30,830,841
Mismatches: 7,468,580 out of 30,830,841
Insertions: 619,226 out of 30,830,841
Identity over aligned base-pairs: 69.9%

Block size distribution

Size range All 219,875 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,334
7.0 kb
10 bp - 100 bp
33,384
2.2 Mb
15,226
1.1 Mb
100 bp - 1 kb
162,898
56.3 Mb
60,231
21.2 Mb
1 kb - 10 kb
21,669
39.2 Mb
23,445
55.7 Mb
10 kb - 100 kb
580
25.4 Mb
858
33.0 Mb
100 kb - 1 Mb
10
1.1 Mb
53
13.5 Mb