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Pythium arrhenomanes vs Phytophthora kernoviae LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes 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 arrhenomanesPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 34,871 alignment blocks

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

Uncovered: 27,718,940 out of 44,672,625
Covered: 16,953,685 out of 44,672,625

Uncovered: 5,441,288 out of 18,367,184
Matches: 8,261,576 out of 18,367,184
Mismatches: 4,190,052 out of 18,367,184
Insertions: 474,268 out of 18,367,184
Identity over aligned base-pairs: 63.9%

Phytophthora kernoviae

Uncovered: 25,920,378 out of 43,208,681
Covered: 17,288,303 out of 43,208,681

Uncovered: 2,852,282 out of 11,344,308
Matches: 5,542,572 out of 11,344,308
Mismatches: 2,704,605 out of 11,344,308
Insertions: 244,849 out of 11,344,308
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 34,871 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
101
585.0 bp
10 bp - 100 bp
3,750
257.8 kb
830
60.6 kb
100 bp - 1 kb
24,966
10.2 Mb
8,633
4.0 Mb
1 kb - 10 kb
6,042
10.1 Mb
5,784
14.6 Mb
10 kb - 100 kb
12
138.6 kb
148
2.1 Mb