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Bigelowiella natans vs Phytophthora kernoviae LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Bigelowiella natans 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

ParameterBigelowiella natansPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,437 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bigelowiella natans

Uncovered: 93,281,198 out of 94,701,163
Covered: 1,419,965 out of 94,701,163

Uncovered: 27,518,516 out of 28,817,508
Matches: 802,761 out of 28,817,508
Mismatches: 456,338 out of 28,817,508
Insertions: 39,893 out of 28,817,508
Identity over aligned base-pairs: 61.8%

Phytophthora kernoviae

Uncovered: 41,629,225 out of 43,208,681
Covered: 1,579,456 out of 43,208,681

Uncovered: 10,238,568 out of 11,344,308
Matches: 674,331 out of 11,344,308
Mismatches: 396,906 out of 11,344,308
Insertions: 34,503 out of 11,344,308
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 7,437 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
28
158.0 bp
10 bp - 100 bp
2,585
181.5 kb
539
38.2 kb
100 bp - 1 kb
4,488
1.2 Mb
2,282
886.6 kb
1 kb - 10 kb
336
541.9 kb
541
978.1 kb
10 kb - 100 kb
6
70.0 kb