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Entamoeba histolytica vs Phytophthora kernoviae LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 histolyticaPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,661 alignment blocks

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

Uncovered: 20,271,614 out of 20,835,395
Covered: 563,781 out of 20,835,395

Uncovered: 9,704,780 out of 10,244,611
Matches: 311,149 out of 10,244,611
Mismatches: 216,540 out of 10,244,611
Insertions: 12,142 out of 10,244,611
Identity over aligned base-pairs: 57.6%

Phytophthora kernoviae

Uncovered: 42,692,548 out of 43,208,681
Covered: 516,133 out of 43,208,681

Uncovered: 10,998,484 out of 11,344,308
Matches: 194,714 out of 11,344,308
Mismatches: 140,214 out of 11,344,308
Insertions: 10,896 out of 11,344,308
Identity over aligned base-pairs: 56.3%

Block size distribution

Size range All 1,661 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
19.0 bp
10 bp - 100 bp
122
8.5 kb
30
2.1 kb
100 bp - 1 kb
1,379
531.2 kb
851
381.5 kb
1 kb - 10 kb
157
221.3 kb
249
377.4 kb