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Phytophthora infestans vs Phytophthora nicotianae P1569 LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Phytophthora nicotianae P1569 (Phytophthora nicotianae P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora infestans 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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

ParameterPhytophthora infestansPhytophthora nicotianae P1569
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 140,359 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

Uncovered: 135,911,489 out of 228,543,505
Covered: 92,632,016 out of 228,543,505

Uncovered: 884,738 out of 22,421,425
Matches: 18,033,786 out of 22,421,425
Mismatches: 3,342,857 out of 22,421,425
Insertions: 160,044 out of 22,421,425
Identity over aligned base-pairs: 83.7%

Phytophthora nicotianae P1569

Uncovered: 11,231,713 out of 55,229,644
Covered: 43,997,931 out of 55,229,644

Uncovered: 1,488,332 out of 27,601,672
Matches: 19,497,530 out of 27,601,672
Mismatches: 6,290,272 out of 27,601,672
Insertions: 325,538 out of 27,601,672
Identity over aligned base-pairs: 74.7%

Block size distribution

Size range All 140,359 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
852
4.7 kb
10 bp - 100 bp
22,460
1.5 Mb
12,909
909.5 kb
100 bp - 1 kb
89,159
32.0 Mb
57,823
21.1 Mb
1 kb - 10 kb
27,199
63.5 Mb
22,085
55.5 Mb
10 kb - 100 kb
689
10.9 Mb
1,402
29.0 Mb
100 kb - 1 Mb
10
1.3 Mb