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Phytophthora ramorum vs Pythium arrhenomanes LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora ramorum 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 ramorumPythium arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 41,995 alignment blocks

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

Uncovered: 44,236,089 out of 66,652,401
Covered: 22,416,312 out of 66,652,401

Uncovered: 7,126,132 out of 22,377,278
Matches: 9,819,830 out of 22,377,278
Mismatches: 4,894,768 out of 22,377,278
Insertions: 536,548 out of 22,377,278
Identity over aligned base-pairs: 64.4%

Pythium arrhenomanes

Uncovered: 25,894,643 out of 44,672,625
Covered: 18,777,982 out of 44,672,625

Uncovered: 4,608,603 out of 18,367,184
Matches: 8,681,052 out of 18,367,184
Mismatches: 4,510,171 out of 18,367,184
Insertions: 567,358 out of 18,367,184
Identity over aligned base-pairs: 63.1%

Block size distribution

Size range All 41,995 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
130
690.0 bp
10 bp - 100 bp
4,233
285.3 kb
1,156
82.2 kb
100 bp - 1 kb
29,707
12.3 Mb
11,685
5.3 Mb
1 kb - 10 kb
7,903
13.9 Mb
7,497
18.6 Mb
10 kb - 100 kb
22
339.9 kb
197
2.8 Mb