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Albugo laibachii vs Pythium iwayamai LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 26,357 alignment blocks

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

Uncovered: 21,277,055 out of 32,766,811
Covered: 11,489,756 out of 32,766,811

Uncovered: 7,774,602 out of 15,902,867
Matches: 4,970,676 out of 15,902,867
Mismatches: 2,940,966 out of 15,902,867
Insertions: 216,623 out of 15,902,867
Identity over aligned base-pairs: 61.2%

Pythium iwayamai

Uncovered: 34,076,048 out of 43,199,174
Covered: 9,123,126 out of 43,199,174

Uncovered: 12,336,200 out of 19,552,457
Matches: 4,410,798 out of 19,552,457
Mismatches: 2,562,960 out of 19,552,457
Insertions: 242,499 out of 19,552,457
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 26,357 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
45
251.0 bp
10 bp - 100 bp
3,003
208.4 kb
1,034
73.1 kb
100 bp - 1 kb
19,760
7.9 Mb
8,509
3.7 Mb
1 kb - 10 kb
3,546
5.6 Mb
4,721
9.4 Mb
10 kb - 100 kb
3
35.6 kb
34
470.7 kb