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Entamoeba histolytica vs Pythium iwayamai LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 793 alignment blocks

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

Uncovered: 20,560,722 out of 20,835,395
Covered: 274,673 out of 20,835,395

Uncovered: 9,982,385 out of 10,244,611
Matches: 147,582 out of 10,244,611
Mismatches: 111,344 out of 10,244,611
Insertions: 3,300 out of 10,244,611
Identity over aligned base-pairs: 56.3%

Pythium iwayamai

Uncovered: 43,001,802 out of 43,199,174
Covered: 197,372 out of 43,199,174

Uncovered: 19,375,361 out of 19,552,457
Matches: 98,604 out of 19,552,457
Mismatches: 74,570 out of 19,552,457
Insertions: 3,922 out of 19,552,457
Identity over aligned base-pairs: 55.7%

Block size distribution

Size range All 793 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
1.0 bp
10 bp - 100 bp
85
6.2 kb
27
2.2 kb
100 bp - 1 kb
665
250.5 kb
412
181.9 kb
1 kb - 10 kb
42
65.9 kb
89
138.5 kb