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Bigelowiella natans vs Phytophthora lateralis LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 natansPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,914 alignment blocks

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

Uncovered: 93,541,150 out of 94,701,163
Covered: 1,160,013 out of 94,701,163

Uncovered: 27,753,523 out of 28,817,508
Matches: 653,589 out of 28,817,508
Mismatches: 376,851 out of 28,817,508
Insertions: 33,545 out of 28,817,508
Identity over aligned base-pairs: 61.4%

Phytophthora lateralis

Uncovered: 42,772,538 out of 43,981,379
Covered: 1,208,841 out of 43,981,379

Uncovered: 13,217,803 out of 14,242,768
Matches: 620,794 out of 14,242,768
Mismatches: 367,843 out of 14,242,768
Insertions: 36,328 out of 14,242,768
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 5,914 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
19
129.0 bp
10 bp - 100 bp
2,041
141.6 kb
466
32.6 kb
100 bp - 1 kb
3,599
1.0 Mb
1,857
720.9 kb
1 kb - 10 kb
255
404.1 kb
406
728.7 kb
10 kb - 100 kb
6
67.8 kb