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Giardia lamblia vs Bigelowiella natans LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Giardia lamblia 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

ParameterGiardia lambliaBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,351 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Giardia lamblia

Uncovered: 10,914,888 out of 11,192,215
Covered: 277,327 out of 11,192,215

Uncovered: 9,050,066 out of 9,322,001
Matches: 159,218 out of 9,322,001
Mismatches: 100,653 out of 9,322,001
Insertions: 12,064 out of 9,322,001
Identity over aligned base-pairs: 58.6%

Bigelowiella natans

Uncovered: 94,337,855 out of 94,701,163
Covered: 363,308 out of 94,701,163

Uncovered: 28,471,363 out of 28,817,508
Matches: 206,889 out of 28,817,508
Mismatches: 128,565 out of 28,817,508
Insertions: 10,691 out of 28,817,508
Identity over aligned base-pairs: 59.8%

Block size distribution

Size range All 1,351 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
25.0 bp
10 bp - 100 bp
309
21.7 kb
96
7.1 kb
100 bp - 1 kb
959
298.5 kb
526
202.2 kb
1 kb - 10 kb
79
119.8 kb
115
230.7 kb