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Giardia lamblia vs Phytophthora parasitica LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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 lambliaPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,601 alignment blocks

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

Uncovered: 10,788,307 out of 11,192,215
Covered: 403,908 out of 11,192,215

Uncovered: 8,925,965 out of 9,322,001
Matches: 230,953 out of 9,322,001
Mismatches: 144,918 out of 9,322,001
Insertions: 20,165 out of 9,322,001
Identity over aligned base-pairs: 58.3%

Phytophthora parasitica

Uncovered: 54,618,280 out of 55,229,644
Covered: 611,364 out of 55,229,644

Uncovered: 27,007,334 out of 27,601,672
Matches: 349,859 out of 27,601,672
Mismatches: 221,943 out of 27,601,672
Insertions: 22,536 out of 27,601,672
Identity over aligned base-pairs: 58.9%

Block size distribution

Size range All 1,601 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
25.0 bp
10 bp - 100 bp
182
13.3 kb
79
6.0 kb
100 bp - 1 kb
1,272
488.9 kb
734
339.1 kb
1 kb - 10 kb
142
209.3 kb
198
366.4 kb