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Pythium vexans vs Phytophthora parasitica LastZ results

Pythium vexans (Pythium vexans DAOM BR484, pve_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 vexans 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 vexansPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,949 alignment blocks

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

Uncovered: 13,203,864 out of 33,844,883
Covered: 20,641,019 out of 33,844,883

Uncovered: 2,796,590 out of 18,608,353
Matches: 10,381,592 out of 18,608,353
Mismatches: 4,829,045 out of 18,608,353
Insertions: 601,126 out of 18,608,353
Identity over aligned base-pairs: 65.7%

Phytophthora parasitica

Uncovered: 30,788,100 out of 55,229,644
Covered: 24,441,544 out of 55,229,644

Uncovered: 7,992,617 out of 27,601,672
Matches: 12,776,688 out of 27,601,672
Mismatches: 6,207,401 out of 27,601,672
Insertions: 624,966 out of 27,601,672
Identity over aligned base-pairs: 65.2%

Block size distribution

Size range All 39,949 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
147
823.0 bp
10 bp - 100 bp
4,062
267.9 kb
1,072
76.9 kb
100 bp - 1 kb
26,674
11.5 Mb
9,434
4.3 Mb
1 kb - 10 kb
9,048
16.4 Mb
6,812
18.1 Mb
10 kb - 100 kb
18
227.9 kb
377
5.8 Mb