In this section

Bigelowiella natans vs Pythium aphanidermatum LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,468 alignment blocks

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

Uncovered: 93,248,407 out of 94,701,163
Covered: 1,452,756 out of 94,701,163

Uncovered: 27,505,686 out of 28,817,508
Matches: 809,099 out of 28,817,508
Mismatches: 463,502 out of 28,817,508
Insertions: 39,221 out of 28,817,508
Identity over aligned base-pairs: 61.7%

Pythium aphanidermatum

Uncovered: 34,324,782 out of 35,876,849
Covered: 1,552,067 out of 35,876,849

Uncovered: 16,634,354 out of 18,015,574
Matches: 839,972 out of 18,015,574
Mismatches: 493,985 out of 18,015,574
Insertions: 47,263 out of 18,015,574
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 7,468 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
35
195.0 bp
10 bp - 100 bp
2,620
181.4 kb
580
41.3 kb
100 bp - 1 kb
4,497
1.3 Mb
2,267
892.0 kb
1 kb - 10 kb
316
507.0 kb
525
970.5 kb
10 kb - 100 kb
5
56.9 kb