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Pythium aphanidermatum vs Phytophthora lateralis LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium aphanidermatum 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 aphanidermatumPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 34,478 alignment blocks

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

Uncovered: 20,338,182 out of 35,876,849
Covered: 15,538,667 out of 35,876,849

Uncovered: 6,102,121 out of 18,015,574
Matches: 7,666,858 out of 18,015,574
Mismatches: 3,805,874 out of 18,015,574
Insertions: 440,721 out of 18,015,574
Identity over aligned base-pairs: 64.4%

Phytophthora lateralis

Uncovered: 26,072,944 out of 43,981,379
Covered: 17,908,435 out of 43,981,379

Uncovered: 3,862,768 out of 14,242,768
Matches: 6,654,266 out of 14,242,768
Mismatches: 3,351,232 out of 14,242,768
Insertions: 374,502 out of 14,242,768
Identity over aligned base-pairs: 64.1%

Block size distribution

Size range All 34,478 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
107
546.0 bp
10 bp - 100 bp
3,341
225.3 kb
920
66.4 kb
100 bp - 1 kb
24,700
10.3 Mb
9,306
4.1 Mb
1 kb - 10 kb
6,318
10.7 Mb
5,576
14.0 Mb
10 kb - 100 kb
12
151.8 kb
215
3.3 Mb