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Pythium iwayamai vs Phytophthora kernoviae LastZ results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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 iwayamaiPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,455 alignment blocks

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

Uncovered: 24,140,758 out of 43,199,174
Covered: 19,058,416 out of 43,199,174

Uncovered: 4,814,186 out of 19,552,457
Matches: 9,540,530 out of 19,552,457
Mismatches: 4,646,613 out of 19,552,457
Insertions: 551,128 out of 19,552,457
Identity over aligned base-pairs: 64.7%

Phytophthora kernoviae

Uncovered: 23,984,397 out of 43,208,681
Covered: 19,224,284 out of 43,208,681

Uncovered: 2,685,159 out of 11,344,308
Matches: 5,819,213 out of 11,344,308
Mismatches: 2,628,275 out of 11,344,308
Insertions: 211,661 out of 11,344,308
Identity over aligned base-pairs: 67.2%

Block size distribution

Size range All 39,455 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
117
619.0 bp
10 bp - 100 bp
4,153
282.6 kb
1,161
82.6 kb
100 bp - 1 kb
28,783
11.7 Mb
10,072
4.3 Mb
1 kb - 10 kb
6,386
11.1 Mb
5,975
15.7 Mb
10 kb - 100 kb
16
196.7 kb
220
3.2 Mb