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Phytophthora infestans vs Pythium arrhenomanes LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 56,192 alignment blocks

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

Uncovered: 199,367,719 out of 228,543,505
Covered: 29,175,786 out of 228,543,505

Uncovered: 6,818,581 out of 22,421,425
Matches: 9,906,931 out of 22,421,425
Mismatches: 5,194,097 out of 22,421,425
Insertions: 501,816 out of 22,421,425
Identity over aligned base-pairs: 63.5%

Pythium arrhenomanes

Uncovered: 27,066,112 out of 44,672,625
Covered: 17,606,513 out of 44,672,625

Uncovered: 5,179,206 out of 18,367,184
Matches: 8,249,042 out of 18,367,184
Mismatches: 4,399,071 out of 18,367,184
Insertions: 539,865 out of 18,367,184
Identity over aligned base-pairs: 62.5%

Block size distribution

Size range All 56,192 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
150
834.0 bp
10 bp - 100 bp
6,201
420.8 kb
2,389
170.6 kb
100 bp - 1 kb
40,611
16.4 Mb
19,404
8.7 Mb
1 kb - 10 kb
9,206
16.3 Mb
9,791
22.7 Mb
10 kb - 100 kb
24
347.1 kb
143
2.1 Mb