In this section

Phytophthora kernoviae vs Phytophthora parasitica LastZ results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora kernoviae 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 kernoviaePhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 37,807 alignment blocks

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

Uncovered: 15,804,940 out of 43,208,681
Covered: 27,403,741 out of 43,208,681

Uncovered: 842,555 out of 11,344,308
Matches: 7,861,037 out of 11,344,308
Mismatches: 2,437,722 out of 11,344,308
Insertions: 202,994 out of 11,344,308
Identity over aligned base-pairs: 74.9%

Phytophthora parasitica

Uncovered: 24,023,628 out of 55,229,644
Covered: 31,206,016 out of 55,229,644

Uncovered: 4,331,024 out of 27,601,672
Matches: 16,571,662 out of 27,601,672
Mismatches: 6,318,379 out of 27,601,672
Insertions: 380,607 out of 27,601,672
Identity over aligned base-pairs: 71.2%

Block size distribution

Size range All 37,807 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
254
1.3 kb
10 bp - 100 bp
4,083
268.5 kb
1,637
117.4 kb
100 bp - 1 kb
22,446
9.4 Mb
11,242
4.8 Mb
1 kb - 10 kb
10,924
24.9 Mb
5,788
14.8 Mb
10 kb - 100 kb
100
1.3 Mb
734
15.6 Mb
100 kb - 1 Mb
4
539.3 kb