Puccinia triticina vs Puccinia graminis LastZ results

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 67. Puccinia triticina 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)
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

Statistics over 2,867 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Puccinia triticina

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
Identity over aligned base-pairs: 84.0%

Puccinia graminis

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
Identity over aligned base-pairs: 83.1%

Block size distribution

Size range All 2,867 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
63.0 bp
10 bp - 100 bp
249
15.7 kb
82
5.0 kb
100 bp - 1 kb
952
407.5 kb
142
41.0 kb
1 kb - 10 kb
1,647
4.5 Mb
760
2.7 Mb
10 kb - 100 kb
8
101.9 kb
117
2.3 Mb