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Pythium vexans vs Phytophthora lateralis LastZ results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 36,136 alignment blocks

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

Uncovered: 15,581,194 out of 33,844,883
Covered: 18,263,689 out of 33,844,883

Uncovered: 4,689,205 out of 18,608,353
Matches: 9,215,346 out of 18,608,353
Mismatches: 4,157,026 out of 18,608,353
Insertions: 546,776 out of 18,608,353
Identity over aligned base-pairs: 66.2%

Phytophthora lateralis

Uncovered: 23,836,968 out of 43,981,379
Covered: 20,144,411 out of 43,981,379

Uncovered: 2,616,242 out of 14,242,768
Matches: 7,880,456 out of 14,242,768
Mismatches: 3,371,659 out of 14,242,768
Insertions: 374,411 out of 14,242,768
Identity over aligned base-pairs: 67.8%

Block size distribution

Size range All 36,136 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
191
943.0 bp
10 bp - 100 bp
3,873
254.9 kb
1,370
96.3 kb
100 bp - 1 kb
24,566
10.3 Mb
9,813
4.2 Mb
1 kb - 10 kb
7,488
13.5 Mb
5,668
15.0 Mb
10 kb - 100 kb
18
239.7 kb
322
4.9 Mb