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Entamoeba histolytica vs Pythium irregulare LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,019 alignment blocks

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

Uncovered: 20,464,792 out of 20,835,395
Covered: 370,603 out of 20,835,395

Uncovered: 9,887,526 out of 10,244,611
Matches: 201,985 out of 10,244,611
Mismatches: 149,635 out of 10,244,611
Insertions: 5,465 out of 10,244,611
Identity over aligned base-pairs: 56.6%

Pythium irregulare

Uncovered: 42,688,190 out of 42,968,084
Covered: 279,894 out of 42,968,084

Uncovered: 20,285,125 out of 20,543,058
Matches: 143,716 out of 20,543,058
Mismatches: 107,723 out of 20,543,058
Insertions: 6,494 out of 20,543,058
Identity over aligned base-pairs: 55.7%

Block size distribution

Size range All 1,019 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
10 bp - 100 bp
78
5.7 kb
24
1.8 kb
100 bp - 1 kb
850
309.6 kb
520
220.6 kb
1 kb - 10 kb
91
132.6 kb
151
225.4 kb