Vitis vinifera vs Coffea canephora LastZ Results

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Vitis vinifera (Vitis vinifera, 12X) and Coffea canephora (Coffea canephora str. DH200-94, AUK_PRJEB4211_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Vitis vinifera 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: 204,390

Genome coverage (bp) Coding exon coverage (bp)
Vitis vinifera

Uncovered: 419,049,495 out of 486,265,422
Covered: 67,215,927 out of 486,265,422

Uncovered: 4,479,346 out of 32,794,161
Matches: 19,674,041 out of 32,794,161
Mismatches: 8,182,144 out of 32,794,161
Insertions: 458,630 out of 32,794,161

Coffea canephora str. DH200-94

Uncovered: 510,895,143 out of 568,611,505
Covered: 57,716,362 out of 568,611,505

Uncovered: 4,287,241 out of 30,830,841
Matches: 18,495,428 out of 30,830,841
Mismatches: 7,501,463 out of 30,830,841
Insertions: 546,709 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

Vitis vinifera 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}