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Pythium iwayamai vs Phytophthora parasitica LastZ results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) 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 parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 48,200 alignment blocks

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

Uncovered: 23,339,272 out of 43,199,174
Covered: 19,859,902 out of 43,199,174

Uncovered: 4,460,825 out of 19,552,457
Matches: 9,773,173 out of 19,552,457
Mismatches: 4,683,884 out of 19,552,457
Insertions: 634,575 out of 19,552,457
Identity over aligned base-pairs: 64.8%

Phytophthora parasitica

Uncovered: 31,755,807 out of 55,229,644
Covered: 23,473,837 out of 55,229,644

Uncovered: 9,270,826 out of 27,601,672
Matches: 11,761,632 out of 27,601,672
Mismatches: 6,013,714 out of 27,601,672
Insertions: 555,500 out of 27,601,672
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 48,200 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
191
971.0 bp
10 bp - 100 bp
4,782
325.1 kb
1,268
92.7 kb
100 bp - 1 kb
35,276
14.4 Mb
14,139
6.2 Mb
1 kb - 10 kb
7,933
13.4 Mb
8,019
19.3 Mb
10 kb - 100 kb
18
232.5 kb
194
2.8 Mb