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Phytophthora ramorum vs Emiliania huxleyi LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 ramorumEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 19,895 alignment blocks

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

Uncovered: 63,296,514 out of 66,652,401
Covered: 3,355,887 out of 66,652,401

Uncovered: 19,551,561 out of 22,377,278
Matches: 1,704,008 out of 22,377,278
Mismatches: 998,427 out of 22,377,278
Insertions: 123,282 out of 22,377,278
Identity over aligned base-pairs: 60.3%

Emiliania huxleyi

Uncovered: 162,935,180 out of 167,675,649
Covered: 4,740,469 out of 167,675,649

Uncovered: 36,359,138 out of 39,740,234
Matches: 2,060,940 out of 39,740,234
Mismatches: 1,149,177 out of 39,740,234
Insertions: 170,979 out of 39,740,234
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 19,895 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
103
601.0 bp
10 bp - 100 bp
4,514
308.6 kb
1,230
84.2 kb
100 bp - 1 kb
14,469
4.4 Mb
7,262
2.9 Mb
1 kb - 10 kb
792
1.4 Mb
1,731
3.1 Mb
10 kb - 100 kb
17
264.5 kb
18
297.8 kb