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Bigelowiella natans vs Pythium irregulare LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,726 alignment blocks

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

Uncovered: 93,260,489 out of 94,701,163
Covered: 1,440,674 out of 94,701,163

Uncovered: 27,492,831 out of 28,817,508
Matches: 821,741 out of 28,817,508
Mismatches: 462,243 out of 28,817,508
Insertions: 40,693 out of 28,817,508
Identity over aligned base-pairs: 62.0%

Pythium irregulare

Uncovered: 41,390,730 out of 42,968,084
Covered: 1,577,354 out of 42,968,084

Uncovered: 19,107,778 out of 20,543,058
Matches: 873,334 out of 20,543,058
Mismatches: 512,106 out of 20,543,058
Insertions: 49,840 out of 20,543,058
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 7,726 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
34
178.0 bp
10 bp - 100 bp
2,742
190.3 kb
608
42.1 kb
100 bp - 1 kb
4,644
1.3 Mb
2,337
886.3 kb
1 kb - 10 kb
306
536.5 kb
519
963.4 kb
10 kb - 100 kb
7
87.3 kb