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Phytophthora ramorum vs Pythium aphanidermatum LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 38,863 alignment blocks

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

Uncovered: 43,361,856 out of 66,652,401
Covered: 23,290,545 out of 66,652,401

Uncovered: 6,906,433 out of 22,377,278
Matches: 9,894,616 out of 22,377,278
Mismatches: 5,014,039 out of 22,377,278
Insertions: 562,190 out of 22,377,278
Identity over aligned base-pairs: 64.0%

Pythium aphanidermatum

Uncovered: 17,159,133 out of 35,876,849
Covered: 18,717,716 out of 35,876,849

Uncovered: 4,009,169 out of 18,015,574
Matches: 8,751,124 out of 18,015,574
Mismatches: 4,755,108 out of 18,015,574
Insertions: 500,173 out of 18,015,574
Identity over aligned base-pairs: 62.5%

Block size distribution

Size range All 38,863 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
112
561.0 bp
10 bp - 100 bp
3,853
259.6 kb
925
65.4 kb
100 bp - 1 kb
26,568
11.4 Mb
9,050
4.2 Mb
1 kb - 10 kb
8,296
15.0 Mb
6,296
16.5 Mb
10 kb - 100 kb
34
512.5 kb
378
6.4 Mb