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Giardia lamblia vs Pythium aphanidermatum LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,573 alignment blocks

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

Uncovered: 10,776,989 out of 11,192,215
Covered: 415,226 out of 11,192,215

Uncovered: 8,915,967 out of 9,322,001
Matches: 231,710 out of 9,322,001
Mismatches: 153,821 out of 9,322,001
Insertions: 20,503 out of 9,322,001
Identity over aligned base-pairs: 57.1%

Pythium aphanidermatum

Uncovered: 35,260,260 out of 35,876,849
Covered: 616,589 out of 35,876,849

Uncovered: 17,466,999 out of 18,015,574
Matches: 322,124 out of 18,015,574
Mismatches: 204,134 out of 18,015,574
Insertions: 22,317 out of 18,015,574
Identity over aligned base-pairs: 58.7%

Block size distribution

Size range All 1,573 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
4.0 bp
10 bp - 100 bp
189
13.2 kb
73
5.2 kb
100 bp - 1 kb
1,224
475.7 kb
734
330.3 kb
1 kb - 10 kb
159
234.6 kb
206
387.9 kb