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Pythium ultimum vs Bigelowiella natans LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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

ParameterPythium ultimumBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,915 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 43,199,988 out of 44,913,582
Covered: 1,713,594 out of 44,913,582

Uncovered: 18,325,886 out of 19,826,256
Matches: 906,150 out of 19,826,256
Mismatches: 544,276 out of 19,826,256
Insertions: 49,944 out of 19,826,256
Identity over aligned base-pairs: 60.4%

Bigelowiella natans

Uncovered: 93,257,244 out of 94,701,163
Covered: 1,443,919 out of 94,701,163

Uncovered: 27,521,455 out of 28,817,508
Matches: 806,976 out of 28,817,508
Mismatches: 450,607 out of 28,817,508
Insertions: 38,470 out of 28,817,508
Identity over aligned base-pairs: 62.3%

Block size distribution

Size range All 7,915 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
37
199.0 bp
10 bp - 100 bp
2,756
190.5 kb
604
42.3 kb
100 bp - 1 kb
4,782
1.3 Mb
2,399
939.8 kb
1 kb - 10 kb
340
571.9 kb
570
1.1 Mb
10 kb - 100 kb
5
59.0 kb