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Pythium ultimum vs Entamoeba histolytica LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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

ParameterPythium ultimumEntamoeba histolytica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,440 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 44,508,014 out of 44,913,582
Covered: 405,568 out of 44,913,582

Uncovered: 19,475,149 out of 19,826,256
Matches: 197,770 out of 19,826,256
Mismatches: 143,085 out of 19,826,256
Insertions: 10,252 out of 19,826,256
Identity over aligned base-pairs: 56.3%

Entamoeba histolytica

Uncovered: 20,392,637 out of 20,835,395
Covered: 442,758 out of 20,835,395

Uncovered: 9,820,915 out of 10,244,611
Matches: 244,061 out of 10,244,611
Mismatches: 172,639 out of 10,244,611
Insertions: 6,996 out of 10,244,611
Identity over aligned base-pairs: 57.6%

Block size distribution

Size range All 1,440 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
10 bp - 100 bp
162
12.2 kb
98
7.6 kb
100 bp - 1 kb
1,170
430.7 kb
687
290.6 kb
1 kb - 10 kb
108
159.1 kb
201
303.7 kb