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Albugo laibachii vs Phytophthora infestans LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Albugo laibachii 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

ParameterAlbugo laibachiiPhytophthora infestans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 34,463 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 21,589,506 out of 32,766,811
Covered: 11,177,305 out of 32,766,811

Uncovered: 7,347,345 out of 15,902,867
Matches: 5,037,884 out of 15,902,867
Mismatches: 3,246,121 out of 15,902,867
Insertions: 271,517 out of 15,902,867
Identity over aligned base-pairs: 58.9%

Phytophthora infestans

Uncovered: 212,843,219 out of 228,543,505
Covered: 15,700,286 out of 228,543,505

Uncovered: 13,455,283 out of 22,421,425
Matches: 5,489,989 out of 22,421,425
Mismatches: 3,184,101 out of 22,421,425
Insertions: 292,052 out of 22,421,425
Identity over aligned base-pairs: 61.2%

Block size distribution

Size range All 34,463 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
68
323.0 bp
10 bp - 100 bp
5,547
426.0 kb
3,074
246.7 kb
100 bp - 1 kb
23,402
9.3 Mb
11,103
4.8 Mb
1 kb - 10 kb
5,417
9.1 Mb
6,329
13.2 Mb
10 kb - 100 kb
29
537.9 kb
73
1.2 Mb