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Pythium ultimum vs Phytophthora parasitica LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) 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 parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 40,813 alignment blocks

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

Uncovered: 23,175,982 out of 44,913,582
Covered: 21,737,600 out of 44,913,582

Uncovered: 3,832,933 out of 19,826,256
Matches: 10,359,838 out of 19,826,256
Mismatches: 4,984,565 out of 19,826,256
Insertions: 648,920 out of 19,826,256
Identity over aligned base-pairs: 64.8%

Phytophthora parasitica

Uncovered: 31,755,668 out of 55,229,644
Covered: 23,473,976 out of 55,229,644

Uncovered: 8,662,283 out of 27,601,672
Matches: 12,108,036 out of 27,601,672
Mismatches: 6,255,474 out of 27,601,672
Insertions: 575,879 out of 27,601,672
Identity over aligned base-pairs: 63.9%

Block size distribution

Size range All 40,813 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
190
947.0 bp
10 bp - 100 bp
4,374
292.0 kb
1,222
87.7 kb
100 bp - 1 kb
27,187
11.3 Mb
8,838
3.8 Mb
1 kb - 10 kb
9,023
16.7 Mb
6,347
17.1 Mb
10 kb - 100 kb
39
522.2 kb
432
7.6 Mb
100 kb - 1 Mb
2
241.4 kb