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Giardia lamblia vs Pythium vexans LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 lambliaPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,677 alignment blocks

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

Uncovered: 10,784,456 out of 11,192,215
Covered: 407,759 out of 11,192,215

Uncovered: 8,923,968 out of 9,322,001
Matches: 233,338 out of 9,322,001
Mismatches: 145,065 out of 9,322,001
Insertions: 19,630 out of 9,322,001
Identity over aligned base-pairs: 58.6%

Pythium vexans

Uncovered: 33,215,856 out of 33,844,883
Covered: 629,027 out of 33,844,883

Uncovered: 18,039,362 out of 18,608,353
Matches: 336,007 out of 18,608,353
Mismatches: 209,106 out of 18,608,353
Insertions: 23,878 out of 18,608,353
Identity over aligned base-pairs: 59.1%

Block size distribution

Size range All 1,677 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
45.0 bp
10 bp - 100 bp
209
15.1 kb
72
5.6 kb
100 bp - 1 kb
1,300
483.5 kb
735
321.7 kb
1 kb - 10 kb
160
251.1 kb
212
412.5 kb
10 kb - 100 kb
1
10.0 kb