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Phytophthora ramorum vs Pythium ultimum LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) 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 ultimum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 42,536 alignment blocks

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

Uncovered: 39,786,875 out of 66,652,401
Covered: 26,865,526 out of 66,652,401

Uncovered: 5,515,275 out of 22,377,278
Matches: 11,079,784 out of 22,377,278
Mismatches: 5,270,959 out of 22,377,278
Insertions: 511,260 out of 22,377,278
Identity over aligned base-pairs: 65.7%

Pythium ultimum

Uncovered: 20,996,496 out of 44,913,582
Covered: 23,917,086 out of 44,913,582

Uncovered: 3,382,588 out of 19,826,256
Matches: 10,203,598 out of 19,826,256
Mismatches: 5,606,099 out of 19,826,256
Insertions: 633,971 out of 19,826,256
Identity over aligned base-pairs: 62.1%

Block size distribution

Size range All 42,536 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
200
984.0 bp
10 bp - 100 bp
4,416
289.4 kb
1,215
84.9 kb
100 bp - 1 kb
28,027
11.8 Mb
8,698
3.8 Mb
1 kb - 10 kb
9,773
19.4 Mb
5,895
15.8 Mb
10 kb - 100 kb
120
2.0 Mb
554
12.5 Mb
100 kb - 1 Mb
9
1.3 Mb