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Phytophthora infestans vs Pythium aphanidermatum LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 52,963 alignment blocks

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

Uncovered: 198,190,220 out of 228,543,505
Covered: 30,353,285 out of 228,543,505

Uncovered: 6,347,347 out of 22,421,425
Matches: 10,205,283 out of 22,421,425
Mismatches: 5,322,161 out of 22,421,425
Insertions: 546,634 out of 22,421,425
Identity over aligned base-pairs: 63.5%

Pythium aphanidermatum

Uncovered: 18,069,741 out of 35,876,849
Covered: 17,807,108 out of 35,876,849

Uncovered: 4,463,368 out of 18,015,574
Matches: 8,417,167 out of 18,015,574
Mismatches: 4,653,415 out of 18,015,574
Insertions: 481,624 out of 18,015,574
Identity over aligned base-pairs: 62.1%

Block size distribution

Size range All 52,963 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
132
676.0 bp
10 bp - 100 bp
5,924
406.9 kb
2,275
166.1 kb
100 bp - 1 kb
36,576
15.3 Mb
15,959
7.3 Mb
1 kb - 10 kb
10,284
17.7 Mb
9,182
21.8 Mb
10 kb - 100 kb
47
721.5 kb
286
4.9 Mb