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Pythium vexans vs Phytophthora kernoviae LastZ results

Pythium vexans (Pythium vexans DAOM BR484, pve_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 vexans 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 vexansPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 33,967 alignment blocks

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

Uncovered: 13,532,736 out of 33,844,883
Covered: 20,312,147 out of 33,844,883

Uncovered: 2,965,717 out of 18,608,353
Matches: 10,243,188 out of 18,608,353
Mismatches: 4,879,054 out of 18,608,353
Insertions: 520,394 out of 18,608,353
Identity over aligned base-pairs: 65.5%

Phytophthora kernoviae

Uncovered: 22,318,212 out of 43,208,681
Covered: 20,890,469 out of 43,208,681

Uncovered: 1,807,381 out of 11,344,308
Matches: 6,511,217 out of 11,344,308
Mismatches: 2,772,473 out of 11,344,308
Insertions: 253,237 out of 11,344,308
Identity over aligned base-pairs: 68.3%

Block size distribution

Size range All 33,967 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
105
541.0 bp
10 bp - 100 bp
3,541
238.8 kb
959
69.1 kb
100 bp - 1 kb
22,432
9.5 Mb
7,059
3.1 Mb
1 kb - 10 kb
7,867
14.3 Mb
5,012
14.1 Mb
10 kb - 100 kb
22
281.0 kb
424
7.1 Mb