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Bigelowiella natans vs Phytophthora parasitica LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) 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 parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,541 alignment blocks

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

Uncovered: 93,305,518 out of 94,701,163
Covered: 1,395,645 out of 94,701,163

Uncovered: 27,537,895 out of 28,817,508
Matches: 792,723 out of 28,817,508
Mismatches: 448,660 out of 28,817,508
Insertions: 38,230 out of 28,817,508
Identity over aligned base-pairs: 62.0%

Phytophthora parasitica

Uncovered: 53,607,448 out of 55,229,644
Covered: 1,622,196 out of 55,229,644

Uncovered: 26,037,198 out of 27,601,672
Matches: 951,398 out of 27,601,672
Mismatches: 559,708 out of 27,601,672
Insertions: 53,368 out of 27,601,672
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 7,541 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
30
163.0 bp
10 bp - 100 bp
2,569
178.7 kb
529
37.3 kb
100 bp - 1 kb
4,597
1.3 Mb
2,326
907.4 kb
1 kb - 10 kb
345
530.6 kb
558
991.9 kb
10 kb - 100 kb
6
65.1 kb