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Hyaloperonospora arabidopsidis vs Phytophthora kernoviae LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 34,673 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 55,883,520 out of 78,897,814
Covered: 23,014,294 out of 78,897,814

Uncovered: 2,166,644 out of 13,171,834
Matches: 7,692,817 out of 13,171,834
Mismatches: 3,074,716 out of 13,171,834
Insertions: 237,657 out of 13,171,834
Identity over aligned base-pairs: 69.9%

Phytophthora kernoviae

Uncovered: 26,571,750 out of 43,208,681
Covered: 16,636,931 out of 43,208,681

Uncovered: 3,030,272 out of 11,344,308
Matches: 5,720,220 out of 11,344,308
Mismatches: 2,440,414 out of 11,344,308
Insertions: 153,402 out of 11,344,308
Identity over aligned base-pairs: 68.8%

Block size distribution

Size range All 34,673 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
216
1.2 kb
10 bp - 100 bp
3,669
243.8 kb
1,206
87.3 kb
100 bp - 1 kb
22,374
9.4 Mb
10,039
4.3 Mb
1 kb - 10 kb
8,369
16.5 Mb
5,755
15.0 Mb
10 kb - 100 kb
45
677.0 kb
384
7.4 Mb