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Giardia lamblia vs Pythium arrhenomanes LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,563 alignment blocks

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

Uncovered: 10,790,893 out of 11,192,215
Covered: 401,322 out of 11,192,215

Uncovered: 8,929,487 out of 9,322,001
Matches: 226,761 out of 9,322,001
Mismatches: 146,130 out of 9,322,001
Insertions: 19,623 out of 9,322,001
Identity over aligned base-pairs: 57.8%

Pythium arrhenomanes

Uncovered: 44,086,069 out of 44,672,625
Covered: 586,556 out of 44,672,625

Uncovered: 17,858,271 out of 18,367,184
Matches: 298,509 out of 18,367,184
Mismatches: 189,483 out of 18,367,184
Insertions: 20,921 out of 18,367,184
Identity over aligned base-pairs: 58.7%

Block size distribution

Size range All 1,563 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
29.0 bp
10 bp - 100 bp
170
12.3 kb
73
5.6 kb
100 bp - 1 kb
1,236
475.4 kb
752
334.5 kb
1 kb - 10 kb
152
223.7 kb
190
361.3 kb
10 kb - 100 kb
1
10.1 kb