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Phytophthora ramorum vs Albugo laibachii LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Albugo laibachii (Albugo laibachii, ENA1) 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 ramorumAlbugo laibachii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 24,313 alignment blocks

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

Uncovered: 54,550,489 out of 66,652,401
Covered: 12,101,912 out of 66,652,401

Uncovered: 13,513,339 out of 22,377,278
Matches: 5,464,585 out of 22,377,278
Mismatches: 3,132,132 out of 22,377,278
Insertions: 267,222 out of 22,377,278
Identity over aligned base-pairs: 61.6%

Albugo laibachii

Uncovered: 21,332,409 out of 32,766,811
Covered: 11,434,402 out of 32,766,811

Uncovered: 7,322,706 out of 15,902,867
Matches: 4,994,945 out of 15,902,867
Mismatches: 3,323,529 out of 15,902,867
Insertions: 261,687 out of 15,902,867
Identity over aligned base-pairs: 58.2%

Block size distribution

Size range All 24,313 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
37
195.0 bp
10 bp - 100 bp
2,411
169.1 kb
558
40.2 kb
100 bp - 1 kb
17,173
7.3 Mb
6,404
3.2 Mb
1 kb - 10 kb
4,662
8.3 Mb
5,164
11.8 Mb
10 kb - 100 kb
30
534.5 kb
71
1.2 Mb