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Phytophthora infestans vs Bigelowiella natans LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora infestans 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

ParameterPhytophthora infestansBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,608 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

Uncovered: 226,392,252 out of 228,543,505
Covered: 2,151,253 out of 228,543,505

Uncovered: 20,851,330 out of 22,421,425
Matches: 953,562 out of 22,421,425
Mismatches: 562,457 out of 22,421,425
Insertions: 54,076 out of 22,421,425
Identity over aligned base-pairs: 60.7%

Bigelowiella natans

Uncovered: 93,195,433 out of 94,701,163
Covered: 1,505,730 out of 94,701,163

Uncovered: 27,513,733 out of 28,817,508
Matches: 797,129 out of 28,817,508
Mismatches: 468,376 out of 28,817,508
Insertions: 38,270 out of 28,817,508
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 8,608 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
35
219.0 bp
10 bp - 100 bp
2,955
206.9 kb
831
60.0 kb
100 bp - 1 kb
5,106
1.4 Mb
2,574
991.4 kb
1 kb - 10 kb
509
931.3 kb
671
1.4 Mb
10 kb - 100 kb
3
42.0 kb
8
105.4 kb