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Phytophthora ramorum vs Phytophthora infestans LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 ramorumPhytophthora infestans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 102,879 alignment blocks

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

Uncovered: 21,361,764 out of 66,652,401
Covered: 45,290,637 out of 66,652,401

Uncovered: 2,083,762 out of 22,377,278
Matches: 13,981,193 out of 22,377,278
Mismatches: 5,936,060 out of 22,377,278
Insertions: 376,263 out of 22,377,278
Identity over aligned base-pairs: 68.9%

Phytophthora infestans

Uncovered: 132,291,109 out of 228,543,505
Covered: 96,252,396 out of 228,543,505

Uncovered: 1,376,307 out of 22,421,425
Matches: 15,215,571 out of 22,421,425
Mismatches: 5,577,211 out of 22,421,425
Insertions: 252,336 out of 22,421,425
Identity over aligned base-pairs: 72.3%

Block size distribution

Size range All 102,879 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
596
3.0 kb
10 bp - 100 bp
10,426
672.2 kb
4,368
306.9 kb
100 bp - 1 kb
63,279
25.8 Mb
34,508
14.5 Mb
1 kb - 10 kb
27,428
66.8 Mb
20,595
55.0 Mb
10 kb - 100 kb
1,150
21.9 Mb
1,432
32.8 Mb
100 kb - 1 Mb
62
12.6 Mb