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Entamoeba histolytica vs Pythium vexans LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Pythium vexans (Pythium vexans DAOM BR484, pve_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 vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 773 alignment blocks

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

Uncovered: 20,549,997 out of 20,835,395
Covered: 285,398 out of 20,835,395

Uncovered: 9,966,477 out of 10,244,611
Matches: 155,864 out of 10,244,611
Mismatches: 118,447 out of 10,244,611
Insertions: 3,823 out of 10,244,611
Identity over aligned base-pairs: 56.0%

Pythium vexans

Uncovered: 33,631,364 out of 33,844,883
Covered: 213,519 out of 33,844,883

Uncovered: 18,410,368 out of 18,608,353
Matches: 109,680 out of 18,608,353
Mismatches: 83,889 out of 18,608,353
Insertions: 4,416 out of 18,608,353
Identity over aligned base-pairs: 55.4%

Block size distribution

Size range All 773 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
10 bp - 100 bp
45
3.2 kb
8
765.0 bp
100 bp - 1 kb
663
239.5 kb
430
173.5 kb
1 kb - 10 kb
65
97.4 kb
109
165.9 kb