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Entamoeba histolytica vs Pythium aphanidermatum LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_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 histolyticaPythium aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,563 alignment blocks

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

Uncovered: 20,317,158 out of 20,835,395
Covered: 518,237 out of 20,835,395

Uncovered: 9,744,641 out of 10,244,611
Matches: 286,507 out of 10,244,611
Mismatches: 204,501 out of 10,244,611
Insertions: 8,962 out of 10,244,611
Identity over aligned base-pairs: 57.3%

Pythium aphanidermatum

Uncovered: 35,437,395 out of 35,876,849
Covered: 439,454 out of 35,876,849

Uncovered: 17,627,185 out of 18,015,574
Matches: 219,391 out of 18,015,574
Mismatches: 156,741 out of 18,015,574
Insertions: 12,257 out of 18,015,574
Identity over aligned base-pairs: 56.5%

Block size distribution

Size range All 1,563 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
11.0 bp
10 bp - 100 bp
159
11.1 kb
37
3.1 kb
100 bp - 1 kb
1,283
494.3 kb
758
338.6 kb
1 kb - 10 kb
119
168.8 kb
218
332.4 kb