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Entamoeba histolytica vs Phytophthora parasitica LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Entamoeba histolytica 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

ParameterEntamoeba histolyticaPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,418 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Entamoeba histolytica

Uncovered: 20,346,790 out of 20,835,395
Covered: 488,605 out of 20,835,395

Uncovered: 9,771,355 out of 10,244,611
Matches: 271,840 out of 10,244,611
Mismatches: 192,628 out of 10,244,611
Insertions: 8,788 out of 10,244,611
Identity over aligned base-pairs: 57.4%

Phytophthora parasitica

Uncovered: 54,782,873 out of 55,229,644
Covered: 446,771 out of 55,229,644

Uncovered: 27,165,278 out of 27,601,672
Matches: 246,332 out of 27,601,672
Mismatches: 176,099 out of 27,601,672
Insertions: 13,963 out of 27,601,672
Identity over aligned base-pairs: 56.4%

Block size distribution

Size range All 1,418 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
40.0 bp
10 bp - 100 bp
98
7.0 kb
23
1.8 kb
100 bp - 1 kb
1,187
464.7 kb
713
327.7 kb
1 kb - 10 kb
126
175.3 kb
214
317.5 kb