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Pythium ultimum vs Phytophthora kernoviae LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium ultimum 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 ultimumPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 38,670 alignment blocks

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

Uncovered: 22,237,457 out of 44,913,582
Covered: 22,676,125 out of 44,913,582

Uncovered: 3,893,288 out of 19,826,256
Matches: 10,318,376 out of 19,826,256
Mismatches: 5,044,751 out of 19,826,256
Insertions: 569,841 out of 19,826,256
Identity over aligned base-pairs: 64.8%

Phytophthora kernoviae

Uncovered: 22,371,008 out of 43,208,681
Covered: 20,837,673 out of 43,208,681

Uncovered: 2,102,365 out of 11,344,308
Matches: 6,165,188 out of 11,344,308
Mismatches: 2,837,436 out of 11,344,308
Insertions: 239,319 out of 11,344,308
Identity over aligned base-pairs: 66.7%

Block size distribution

Size range All 38,670 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
125
638.0 bp
10 bp - 100 bp
4,131
276.5 kb
1,164
81.7 kb
100 bp - 1 kb
26,096
11.0 Mb
8,388
3.7 Mb
1 kb - 10 kb
8,285
15.3 Mb
5,230
13.6 Mb
10 kb - 100 kb
33
451.5 kb
479
9.3 Mb
100 kb - 1 Mb
2
259.8 kb