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Phytophthora ramorum vs Giardia lamblia LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Giardia lamblia (Giardia lamblia, GL2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora ramorum 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 ramorumGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,709 alignment blocks

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

Uncovered: 65,950,187 out of 66,652,401
Covered: 702,214 out of 66,652,401

Uncovered: 21,757,198 out of 22,377,278
Matches: 368,187 out of 22,377,278
Mismatches: 228,501 out of 22,377,278
Insertions: 23,392 out of 22,377,278
Identity over aligned base-pairs: 59.4%

Giardia lamblia

Uncovered: 10,739,099 out of 11,192,215
Covered: 453,116 out of 11,192,215

Uncovered: 8,886,372 out of 9,322,001
Matches: 233,189 out of 9,322,001
Mismatches: 182,628 out of 9,322,001
Insertions: 19,812 out of 9,322,001
Identity over aligned base-pairs: 53.5%

Block size distribution

Size range All 1,709 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
19.0 bp
10 bp - 100 bp
229
16.8 kb
116
8.8 kb
100 bp - 1 kb
1,289
494.8 kb
779
341.2 kb
1 kb - 10 kb
187
293.1 kb
229
454.8 kb
10 kb - 100 kb
1
13.3 kb
1
13.3 kb