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Albugo laibachii vs Pythium aphanidermatum LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) 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 laibachiiPythium aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 20,141 alignment blocks

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

Uncovered: 22,254,855 out of 32,766,811
Covered: 10,511,956 out of 32,766,811

Uncovered: 7,480,725 out of 15,902,867
Matches: 5,124,907 out of 15,902,867
Mismatches: 3,024,566 out of 15,902,867
Insertions: 272,669 out of 15,902,867
Identity over aligned base-pairs: 60.9%

Pythium aphanidermatum

Uncovered: 26,758,652 out of 35,876,849
Covered: 9,118,197 out of 35,876,849

Uncovered: 10,445,181 out of 18,015,574
Matches: 4,660,625 out of 18,015,574
Mismatches: 2,667,662 out of 18,015,574
Insertions: 242,106 out of 18,015,574
Identity over aligned base-pairs: 61.6%

Block size distribution

Size range All 20,141 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
33
203.0 bp
10 bp - 100 bp
2,030
142.0 kb
320
23.2 kb
100 bp - 1 kb
14,433
6.2 Mb
4,697
2.4 Mb
1 kb - 10 kb
3,639
5.9 Mb
4,084
9.3 Mb
10 kb - 100 kb
6
70.0 kb
44
598.7 kb