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Bigelowiella natans vs Pythium arrhenomanes LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_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 natansPythium arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,966 alignment blocks

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

Uncovered: 93,360,898 out of 94,701,163
Covered: 1,340,265 out of 94,701,163

Uncovered: 27,583,256 out of 28,817,508
Matches: 757,380 out of 28,817,508
Mismatches: 440,829 out of 28,817,508
Insertions: 36,043 out of 28,817,508
Identity over aligned base-pairs: 61.4%

Pythium arrhenomanes

Uncovered: 43,239,416 out of 44,672,625
Covered: 1,433,209 out of 44,672,625

Uncovered: 17,124,165 out of 18,367,184
Matches: 752,609 out of 18,367,184
Mismatches: 446,977 out of 18,367,184
Insertions: 43,433 out of 18,367,184
Identity over aligned base-pairs: 60.5%

Block size distribution

Size range All 6,966 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
37
208.0 bp
10 bp - 100 bp
2,335
163.0 kb
503
35.8 kb
100 bp - 1 kb
4,312
1.2 Mb
2,289
863.2 kb
1 kb - 10 kb
282
472.6 kb
481
897.9 kb
10 kb - 100 kb
2
21.6 kb