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Phytophthora ramorum vs Phytophthora kernoviae LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora ramorum 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 ramorumPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 38,344 alignment blocks

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

Uncovered: 31,124,717 out of 66,652,401
Covered: 35,527,684 out of 66,652,401

Uncovered: 2,846,935 out of 22,377,278
Matches: 14,405,095 out of 22,377,278
Mismatches: 4,830,417 out of 22,377,278
Insertions: 294,831 out of 22,377,278
Identity over aligned base-pairs: 73.8%

Phytophthora kernoviae

Uncovered: 14,667,415 out of 43,208,681
Covered: 28,541,266 out of 43,208,681

Uncovered: 863,967 out of 11,344,308
Matches: 7,583,836 out of 11,344,308
Mismatches: 2,715,923 out of 11,344,308
Insertions: 180,582 out of 11,344,308
Identity over aligned base-pairs: 72.4%

Block size distribution

Size range All 38,344 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
233
1.2 kb
10 bp - 100 bp
4,179
276.2 kb
1,732
126.0 kb
100 bp - 1 kb
22,035
9.2 Mb
10,863
4.7 Mb
1 kb - 10 kb
11,736
28.4 Mb
5,588
14.2 Mb
10 kb - 100 kb
161
2.5 Mb
666
18.5 Mb
100 kb - 1 Mb
22
2.9 Mb