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Phytophthora infestans vs Giardia lamblia LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Giardia lamblia (Giardia lamblia, GL2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora infestans 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

ParameterPhytophthora infestansGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,081 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

Uncovered: 227,645,141 out of 228,543,505
Covered: 898,364 out of 228,543,505

Uncovered: 21,816,407 out of 22,421,425
Matches: 357,519 out of 22,421,425
Mismatches: 224,918 out of 22,421,425
Insertions: 22,581 out of 22,421,425
Identity over aligned base-pairs: 59.1%

Giardia lamblia

Uncovered: 10,757,872 out of 11,192,215
Covered: 434,343 out of 11,192,215

Uncovered: 8,899,429 out of 9,322,001
Matches: 229,034 out of 9,322,001
Mismatches: 173,828 out of 9,322,001
Insertions: 19,710 out of 9,322,001
Identity over aligned base-pairs: 54.2%

Block size distribution

Size range All 4,081 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
17.0 bp
10 bp - 100 bp
1,889
150.8 kb
1,789
143.9 kb
100 bp - 1 kb
2,034
592.2 kb
1,525
445.8 kb
1 kb - 10 kb
154
258.4 kb
200
403.0 kb
10 kb - 100 kb
1
15.1 kb
1
23.9 kb