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Phytophthora infestans vs Pythium irregulare LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora infestans 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

ParameterPhytophthora infestansPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 52,586 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

Uncovered: 200,744,790 out of 228,543,505
Covered: 27,798,715 out of 228,543,505

Uncovered: 5,342,921 out of 22,421,425
Matches: 11,264,951 out of 22,421,425
Mismatches: 5,358,069 out of 22,421,425
Insertions: 455,484 out of 22,421,425
Identity over aligned base-pairs: 66.0%

Pythium irregulare

Uncovered: 22,902,153 out of 42,968,084
Covered: 20,065,931 out of 42,968,084

Uncovered: 4,800,440 out of 20,543,058
Matches: 9,885,768 out of 20,543,058
Mismatches: 5,147,374 out of 20,543,058
Insertions: 709,476 out of 20,543,058
Identity over aligned base-pairs: 62.8%

Block size distribution

Size range All 52,586 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
212
1.0 kb
10 bp - 100 bp
6,086
416.4 kb
2,364
171.6 kb
100 bp - 1 kb
37,032
15.1 Mb
16,133
7.3 Mb
1 kb - 10 kb
9,207
16.1 Mb
8,224
19.2 Mb
10 kb - 100 kb
49
754.1 kb
336
5.8 Mb