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Phytophthora ramorum vs Phytophthora lateralis LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 74,755 alignment blocks

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

Uncovered: 16,056,989 out of 66,652,401
Covered: 50,595,412 out of 66,652,401

Uncovered: 3,661,698 out of 22,377,278
Matches: 16,915,309 out of 22,377,278
Mismatches: 1,652,626 out of 22,377,278
Insertions: 147,645 out of 22,377,278
Identity over aligned base-pairs: 90.4%

Phytophthora lateralis

Uncovered: 4,847,022 out of 43,981,379
Covered: 39,134,357 out of 43,981,379

Uncovered: 357,540 out of 14,242,768
Matches: 11,902,313 out of 14,242,768
Mismatches: 1,929,596 out of 14,242,768
Insertions: 53,319 out of 14,242,768
Identity over aligned base-pairs: 85.7%

Block size distribution

Size range All 74,755 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
759
4.1 kb
10 bp - 100 bp
14,005
861.7 kb
6,758
439.1 kb
100 bp - 1 kb
47,348
17.3 Mb
25,196
9.7 Mb
1 kb - 10 kb
11,774
29.9 Mb
10,272
27.0 Mb
10 kb - 100 kb
869
14.6 Mb
992
24.6 Mb
100 kb - 1 Mb
7
824.2 kb