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Albugo laibachii vs Phytophthora kernoviae LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 20,957 alignment blocks

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

Uncovered: 22,518,541 out of 32,766,811
Covered: 10,248,270 out of 32,766,811

Uncovered: 7,603,457 out of 15,902,867
Matches: 5,108,188 out of 15,902,867
Mismatches: 2,932,766 out of 15,902,867
Insertions: 258,456 out of 15,902,867
Identity over aligned base-pairs: 61.5%

Phytophthora kernoviae

Uncovered: 33,438,908 out of 43,208,681
Covered: 9,769,773 out of 43,208,681

Uncovered: 5,754,807 out of 11,344,308
Matches: 3,476,320 out of 11,344,308
Mismatches: 1,948,017 out of 11,344,308
Insertions: 165,164 out of 11,344,308
Identity over aligned base-pairs: 62.2%

Block size distribution

Size range All 20,957 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
40
241.0 bp
10 bp - 100 bp
2,025
141.0 kb
425
30.9 kb
100 bp - 1 kb
15,214
6.5 Mb
5,440
2.7 Mb
1 kb - 10 kb
3,673
6.0 Mb
4,239
9.3 Mb
10 kb - 100 kb
5
56.2 kb
49
653.8 kb