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Puccinia graminis vs Puccinia triticina - GCA_000151525.2 LastZ results

Puccinia graminis (Puccinia graminis f. sp. tritici CRL 75-36-700-3, ASM14992v1) and Puccinia triticina - GCA_000151525.2 (Puccinia triticina, GCA000151525v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 114. 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 - GCA_000151525.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 97,835 alignment blocks

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

Uncovered: 36,731,422 out of 88,724,376
Covered: 51,992,954 out of 88,724,376

Uncovered: 2,264,099 out of 18,687,338
Matches: 11,308,708 out of 18,687,338
Mismatches: 4,670,226 out of 18,687,338
Insertions: 444,305 out of 18,687,338
Identity over aligned base-pairs: 68.9%

Puccinia triticina - GCA_000151525.2

Uncovered: 87,265,240 out of 135,343,689
Covered: 48,078,449 out of 135,343,689

Uncovered: 3,113,591 out of 17,522,293
Matches: 10,594,327 out of 17,522,293
Mismatches: 3,540,334 out of 17,522,293
Insertions: 274,041 out of 17,522,293
Identity over aligned base-pairs: 73.5%

Block size distribution

Size range All 97,835 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
564
3.0 kb
10 bp - 100 bp
13,049
875.5 kb
7,202
511.8 kb
100 bp - 1 kb
62,642
22.8 Mb
37,854
13.9 Mb
1 kb - 10 kb
21,187
48.6 Mb
14,993
40.3 Mb
10 kb - 100 kb
393
7.3 Mb
803
21.3 Mb
100 kb - 1 Mb
25
3.6 Mb