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Giardia lamblia vs Pythium iwayamai LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,697 alignment blocks

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

Uncovered: 10,799,027 out of 11,192,215
Covered: 393,188 out of 11,192,215

Uncovered: 8,941,207 out of 9,322,001
Matches: 221,627 out of 9,322,001
Mismatches: 140,366 out of 9,322,001
Insertions: 18,801 out of 9,322,001
Identity over aligned base-pairs: 58.2%

Pythium iwayamai

Uncovered: 42,614,864 out of 43,199,174
Covered: 584,310 out of 43,199,174

Uncovered: 19,046,597 out of 19,552,457
Matches: 300,108 out of 19,552,457
Mismatches: 185,174 out of 19,552,457
Insertions: 20,578 out of 19,552,457
Identity over aligned base-pairs: 59.3%

Block size distribution

Size range All 1,697 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
15.0 bp
10 bp - 100 bp
231
15.7 kb
97
7.2 kb
100 bp - 1 kb
1,330
478.8 kb
780
343.6 kb
1 kb - 10 kb
133
200.4 kb
167
344.1 kb