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Pythium ultimum vs Phytophthora infestans LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium ultimum 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

ParameterPythium ultimumPhytophthora infestans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 55,970 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 21,924,286 out of 44,913,582
Covered: 22,989,296 out of 44,913,582

Uncovered: 3,959,225 out of 19,826,256
Matches: 9,822,764 out of 19,826,256
Mismatches: 5,424,426 out of 19,826,256
Insertions: 619,841 out of 19,826,256
Identity over aligned base-pairs: 61.9%

Phytophthora infestans

Uncovered: 196,547,620 out of 228,543,505
Covered: 31,995,885 out of 228,543,505

Uncovered: 5,275,369 out of 22,421,425
Matches: 11,160,332 out of 22,421,425
Mismatches: 5,498,324 out of 22,421,425
Insertions: 487,400 out of 22,421,425
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 55,970 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
397
1.8 kb
10 bp - 100 bp
6,289
411.6 kb
1,860
133.8 kb
100 bp - 1 kb
38,663
15.4 Mb
15,541
6.7 Mb
1 kb - 10 kb
10,468
20.3 Mb
8,216
20.5 Mb
10 kb - 100 kb
153
2.5 Mb
489
10.0 Mb
100 kb - 1 Mb
8
1.4 Mb