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Phytophthora infestans vs Pythium iwayamai LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_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
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

ParameterPhytophthora infestansPythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 68,104 alignment blocks

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

Uncovered: 196,273,943 out of 228,543,505
Covered: 32,269,562 out of 228,543,505

Uncovered: 6,059,468 out of 22,421,425
Matches: 10,663,359 out of 22,421,425
Mismatches: 5,247,032 out of 22,421,425
Insertions: 451,566 out of 22,421,425
Identity over aligned base-pairs: 65.2%

Pythium iwayamai

Uncovered: 23,661,361 out of 43,199,174
Covered: 19,537,813 out of 43,199,174

Uncovered: 4,761,357 out of 19,552,457
Matches: 9,358,148 out of 19,552,457
Mismatches: 4,816,413 out of 19,552,457
Insertions: 616,539 out of 19,552,457
Identity over aligned base-pairs: 63.3%

Block size distribution

Size range All 68,104 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
291
1.2 kb
10 bp - 100 bp
8,016
552.2 kb
3,772
273.1 kb
100 bp - 1 kb
49,711
19.2 Mb
24,846
10.0 Mb
1 kb - 10 kb
10,051
17.0 Mb
10,661
23.6 Mb
10 kb - 100 kb
35
550.3 kb
232
3.4 Mb