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Phytophthora infestans vs Pythium vexans LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Pythium vexans (Pythium vexans DAOM BR484, pve_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 vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 49,494 alignment blocks

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

Uncovered: 197,430,081 out of 228,543,505
Covered: 31,113,424 out of 228,543,505

Uncovered: 4,771,241 out of 22,421,425
Matches: 11,644,499 out of 22,421,425
Mismatches: 5,489,985 out of 22,421,425
Insertions: 515,700 out of 22,421,425
Identity over aligned base-pairs: 66.0%

Pythium vexans

Uncovered: 13,522,034 out of 33,844,883
Covered: 20,322,849 out of 33,844,883

Uncovered: 3,059,160 out of 18,608,353
Matches: 9,884,088 out of 18,608,353
Mismatches: 5,072,333 out of 18,608,353
Insertions: 592,772 out of 18,608,353
Identity over aligned base-pairs: 63.6%

Block size distribution

Size range All 49,494 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
121
670.0 bp
10 bp - 100 bp
4,769
315.3 kb
1,495
101.5 kb
100 bp - 1 kb
33,759
14.3 Mb
14,005
6.3 Mb
1 kb - 10 kb
10,797
20.0 Mb
8,814
22.0 Mb
10 kb - 100 kb
48
753.0 kb
409
6.9 Mb