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Phytophthora infestans vs Phytophthora kernoviae LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora infestans 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

ParameterPhytophthora infestansPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 52,702 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

Uncovered: 188,974,257 out of 228,543,505
Covered: 39,569,248 out of 228,543,505

Uncovered: 2,268,375 out of 22,421,425
Matches: 14,597,069 out of 22,421,425
Mismatches: 5,305,168 out of 22,421,425
Insertions: 250,813 out of 22,421,425
Identity over aligned base-pairs: 72.4%

Phytophthora kernoviae

Uncovered: 16,090,077 out of 43,208,681
Covered: 27,118,604 out of 43,208,681

Uncovered: 985,032 out of 11,344,308
Matches: 7,302,867 out of 11,344,308
Mismatches: 2,852,976 out of 11,344,308
Insertions: 203,433 out of 11,344,308
Identity over aligned base-pairs: 70.5%

Block size distribution

Size range All 52,702 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
257
1.4 kb
10 bp - 100 bp
6,146
408.1 kb
3,257
229.5 kb
100 bp - 1 kb
33,177
13.7 Mb
18,576
7.8 Mb
1 kb - 10 kb
12,960
28.0 Mb
8,026
18.7 Mb
10 kb - 100 kb
162
2.6 Mb
633
16.0 Mb
100 kb - 1 Mb
15
2.0 Mb