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Pythium ultimum vs Giardia lamblia LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Giardia lamblia (Giardia lamblia, GL2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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

ParameterPythium ultimumGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,877 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 44,250,586 out of 44,913,582
Covered: 662,996 out of 44,913,582

Uncovered: 19,270,390 out of 19,826,256
Matches: 327,521 out of 19,826,256
Mismatches: 205,858 out of 19,826,256
Insertions: 22,487 out of 19,826,256
Identity over aligned base-pairs: 58.9%

Giardia lamblia

Uncovered: 10,784,520 out of 11,192,215
Covered: 407,695 out of 11,192,215

Uncovered: 8,930,697 out of 9,322,001
Matches: 223,618 out of 9,322,001
Mismatches: 149,379 out of 9,322,001
Insertions: 18,307 out of 9,322,001
Identity over aligned base-pairs: 57.1%

Block size distribution

Size range All 1,877 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
6.0 bp
10 bp - 100 bp
303
21.9 kb
160
12.4 kb
100 bp - 1 kb
1,414
511.5 kb
837
347.0 kb
1 kb - 10 kb
157
230.2 kb
204
394.0 kb
10 kb - 100 kb
2
25.6 kb
2
35.9 kb