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Bigelowiella natans vs Giardia intestinalis - GCA_000002435.2 LastZ results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. 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 natansGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,357 alignment blocks

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

Uncovered: 94,334,999 out of 94,701,163
Covered: 366,164 out of 94,701,163

Uncovered: 28,468,419 out of 28,817,508
Matches: 208,559 out of 28,817,508
Mismatches: 129,638 out of 28,817,508
Insertions: 10,892 out of 28,817,508
Identity over aligned base-pairs: 59.7%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,801,344 out of 12,078,186
Covered: 276,842 out of 12,078,186

Uncovered: 9,194,964 out of 9,469,365
Matches: 160,660 out of 9,469,365
Mismatches: 101,635 out of 9,469,365
Insertions: 12,106 out of 9,469,365
Identity over aligned base-pairs: 58.5%

Block size distribution

Size range All 1,357 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
17.0 bp
10 bp - 100 bp
307
21.6 kb
90
6.7 kb
100 bp - 1 kb
967
302.8 kb
531
205.6 kb
1 kb - 10 kb
80
120.9 kb
117
233.0 kb