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Albugo laibachii vs Pythium irregulare LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 27,581 alignment blocks

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

Uncovered: 20,519,926 out of 32,766,811
Covered: 12,246,885 out of 32,766,811

Uncovered: 7,173,214 out of 15,902,867
Matches: 5,430,254 out of 15,902,867
Mismatches: 3,062,614 out of 15,902,867
Insertions: 236,785 out of 15,902,867
Identity over aligned base-pairs: 62.2%

Pythium irregulare

Uncovered: 32,790,036 out of 42,968,084
Covered: 10,178,048 out of 42,968,084

Uncovered: 12,455,079 out of 20,543,058
Matches: 4,961,293 out of 20,543,058
Mismatches: 2,843,672 out of 20,543,058
Insertions: 283,014 out of 20,543,058
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 27,581 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
99
546.0 bp
10 bp - 100 bp
3,585
243.4 kb
1,157
80.7 kb
100 bp - 1 kb
19,665
7.9 Mb
8,115
3.7 Mb
1 kb - 10 kb
4,226
6.7 Mb
5,045
10.5 Mb
10 kb - 100 kb
6
75.2 kb
47
656.4 kb