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Puccinia graminis vs Puccinia triticina LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Puccinia triticina (Puccinia triticina 1-1 BBBD Race 1, ASM15152v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. Puccinia graminis 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

ParameterPuccinia graminisPuccinia triticina
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 201,418 alignment blocks

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

Uncovered: 15,340,824 out of 88,724,376
Covered: 73,383,552 out of 88,724,376

Uncovered: 1,297,047 out of 18,687,338
Matches: 9,892,142 out of 18,687,338
Mismatches: 7,120,343 out of 18,687,338
Insertions: 377,806 out of 18,687,338
Identity over aligned base-pairs: 56.9%

Puccinia triticina

Uncovered: 47,374,784 out of 162,948,716
Covered: 115,573,932 out of 162,948,716

Uncovered: 1,214,651 out of 13,973,123
Matches: 8,990,022 out of 13,973,123
Mismatches: 3,528,294 out of 13,973,123
Insertions: 240,156 out of 13,973,123
Identity over aligned base-pairs: 70.5%

Block size distribution

Size range All 201,418 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,823
8.6 kb
10 bp - 100 bp
30,172
2.0 Mb
17,922
1.2 Mb
100 bp - 1 kb
130,474
45.9 Mb
84,284
30.8 Mb
1 kb - 10 kb
37,435
88.7 Mb
29,223
79.8 Mb
10 kb - 100 kb
1,512
30.1 Mb
2,340
51.2 Mb
100 kb - 1 Mb
2
206.8 kb
29
3.9 Mb