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Pythium irregulare vs Phytophthora kernoviae LastZ results

Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare 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 irregularePhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 36,521 alignment blocks

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

Uncovered: 22,907,591 out of 42,968,084
Covered: 20,060,493 out of 42,968,084

Uncovered: 4,629,956 out of 20,543,058
Matches: 10,269,502 out of 20,543,058
Mismatches: 4,981,195 out of 20,543,058
Insertions: 662,405 out of 20,543,058
Identity over aligned base-pairs: 64.5%

Phytophthora kernoviae

Uncovered: 23,102,442 out of 43,208,681
Covered: 20,106,239 out of 43,208,681

Uncovered: 2,142,427 out of 11,344,308
Matches: 6,260,807 out of 11,344,308
Mismatches: 2,717,559 out of 11,344,308
Insertions: 223,515 out of 11,344,308
Identity over aligned base-pairs: 68.0%

Block size distribution

Size range All 36,521 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
117
613.0 bp
10 bp - 100 bp
3,922
266.5 kb
885
63.2 kb
100 bp - 1 kb
25,144
10.5 Mb
7,696
3.5 Mb
1 kb - 10 kb
7,312
13.0 Mb
5,434
14.7 Mb
10 kb - 100 kb
26
323.2 kb
358
5.9 Mb