Puccinia triticina vs Puccinia graminis LastZ Results

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Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) and Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 77. Puccinia triticina 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: 2,867

Genome coverage (bp) Coding exon coverage (bp)
Puccinia triticina 1-1 BBBD Race 1

Uncovered: 158,169,051 out of 162,948,716
Covered: 4,779,665 out of 162,948,716

Uncovered: 11,670,329 out of 13,973,123
Matches: 1,934,303 out of 13,973,123
Mismatches: 352,597 out of 13,973,123
Insertions: 15,894 out of 13,973,123

Puccinia graminis f. sp. tritici CRL 75-36-700-3

Uncovered: 84,678,321 out of 88,724,376
Covered: 4,046,055 out of 88,724,376

Uncovered: 16,166,418 out of 18,687,338
Matches: 2,095,111 out of 18,687,338
Mismatches: 394,605 out of 18,687,338
Insertions: 31,204 out of 18,687,338

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)