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Bigelowiella natans vs Pythium vexans LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Pythium vexans (Pythium vexans DAOM BR484, pve_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 vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,641 alignment blocks

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

Uncovered: 93,298,086 out of 94,701,163
Covered: 1,403,077 out of 94,701,163

Uncovered: 27,523,200 out of 28,817,508
Matches: 804,765 out of 28,817,508
Mismatches: 451,411 out of 28,817,508
Insertions: 38,132 out of 28,817,508
Identity over aligned base-pairs: 62.2%

Pythium vexans

Uncovered: 32,287,732 out of 33,844,883
Covered: 1,557,151 out of 33,844,883

Uncovered: 17,202,955 out of 18,608,353
Matches: 860,976 out of 18,608,353
Mismatches: 494,310 out of 18,608,353
Insertions: 50,112 out of 18,608,353
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 7,641 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
42
241.0 bp
10 bp - 100 bp
2,710
187.1 kb
571
39.6 kb
100 bp - 1 kb
4,574
1.3 Mb
2,330
906.4 kb
1 kb - 10 kb
315
499.9 kb
499
920.1 kb
10 kb - 100 kb
7
79.2 kb