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Pythium aphanidermatum vs Phytophthora kernoviae LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 33,187 alignment blocks

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

Uncovered: 18,582,833 out of 35,876,849
Covered: 17,294,016 out of 35,876,849

Uncovered: 4,524,627 out of 18,015,574
Matches: 8,672,236 out of 18,015,574
Mismatches: 4,378,720 out of 18,015,574
Insertions: 439,991 out of 18,015,574
Identity over aligned base-pairs: 64.3%

Phytophthora kernoviae

Uncovered: 25,107,410 out of 43,208,681
Covered: 18,101,271 out of 43,208,681

Uncovered: 2,698,874 out of 11,344,308
Matches: 5,650,013 out of 11,344,308
Mismatches: 2,727,618 out of 11,344,308
Insertions: 267,803 out of 11,344,308
Identity over aligned base-pairs: 65.4%

Block size distribution

Size range All 33,187 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
93
474.0 bp
10 bp - 100 bp
3,484
233.9 kb
681
48.3 kb
100 bp - 1 kb
23,090
9.6 Mb
6,653
3.1 Mb
1 kb - 10 kb
6,506
11.2 Mb
4,954
13.2 Mb
10 kb - 100 kb
14
177.8 kb
298
4.9 Mb