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Phytophthora ramorum vs Phytophthora parasitica LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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 ramorumPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 55,502 alignment blocks

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

Uncovered: 24,043,351 out of 66,652,401
Covered: 42,609,050 out of 66,652,401

Uncovered: 1,870,548 out of 22,377,278
Matches: 15,626,894 out of 22,377,278
Mismatches: 4,499,259 out of 22,377,278
Insertions: 380,577 out of 22,377,278
Identity over aligned base-pairs: 76.2%

Phytophthora parasitica

Uncovered: 15,907,988 out of 55,229,644
Covered: 39,321,656 out of 55,229,644

Uncovered: 2,250,608 out of 27,601,672
Matches: 17,887,440 out of 27,601,672
Mismatches: 7,046,027 out of 27,601,672
Insertions: 417,597 out of 27,601,672
Identity over aligned base-pairs: 70.6%

Block size distribution

Size range All 55,502 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
345
1.7 kb
10 bp - 100 bp
6,402
415.6 kb
2,751
196.7 kb
100 bp - 1 kb
32,878
13.3 Mb
17,995
7.6 Mb
1 kb - 10 kb
15,592
37.7 Mb
9,893
24.9 Mb
10 kb - 100 kb
285
4.1 Mb
922
21.5 Mb
100 kb - 1 Mb
10
1.3 Mb