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Bigelowiella natans vs Pythium iwayamai LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,298 alignment blocks

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

Uncovered: 93,341,400 out of 94,701,163
Covered: 1,359,763 out of 94,701,163

Uncovered: 27,580,312 out of 28,817,508
Matches: 764,668 out of 28,817,508
Mismatches: 435,544 out of 28,817,508
Insertions: 36,984 out of 28,817,508
Identity over aligned base-pairs: 61.8%

Pythium iwayamai

Uncovered: 41,737,562 out of 43,199,174
Covered: 1,461,612 out of 43,199,174

Uncovered: 18,274,052 out of 19,552,457
Matches: 782,586 out of 19,552,457
Mismatches: 449,642 out of 19,552,457
Insertions: 46,177 out of 19,552,457
Identity over aligned base-pairs: 61.2%

Block size distribution

Size range All 7,298 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
24
100.0 bp
10 bp - 100 bp
2,471
172.2 kb
543
38.6 kb
100 bp - 1 kb
4,536
1.2 Mb
2,402
907.3 kb
1 kb - 10 kb
267
460.7 kb
444
824.9 kb
10 kb - 100 kb
7
83.7 kb