Solanum lycopersicum vs Coffea canephora LastZ Results

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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 . Solanum lycopersicum was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 219,875

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

Coffea canephora str. DH200-94

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

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Solanum lycopersicum Coffea canephora
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}