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Entamoeba histolytica vs Emiliania huxleyi LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 histolyticaEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,010 alignment blocks

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

Uncovered: 20,697,353 out of 20,835,395
Covered: 138,042 out of 20,835,395

Uncovered: 10,120,718 out of 10,244,611
Matches: 70,764 out of 10,244,611
Mismatches: 52,233 out of 10,244,611
Insertions: 896 out of 10,244,611
Identity over aligned base-pairs: 57.1%

Emiliania huxleyi

Uncovered: 167,451,198 out of 167,675,649
Covered: 224,451 out of 167,675,649

Uncovered: 39,586,273 out of 39,740,234
Matches: 90,047 out of 39,740,234
Mismatches: 62,315 out of 39,740,234
Insertions: 1,599 out of 39,740,234
Identity over aligned base-pairs: 58.5%

Block size distribution

Size range All 1,010 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
15.0 bp
10 bp - 100 bp
214
16.6 kb
57
4.7 kb
100 bp - 1 kb
724
220.4 kb
441
160.2 kb
1 kb - 10 kb
57
72.0 kb
90
144.1 kb