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Entamoeba histolytica vs Phytophthora infestans LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 infestans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,944 alignment blocks

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

Uncovered: 20,308,662 out of 20,835,395
Covered: 526,733 out of 20,835,395

Uncovered: 9,753,794 out of 10,244,611
Matches: 263,700 out of 10,244,611
Mismatches: 219,149 out of 10,244,611
Insertions: 7,968 out of 10,244,611
Identity over aligned base-pairs: 53.7%

Phytophthora infestans

Uncovered: 227,890,077 out of 228,543,505
Covered: 653,428 out of 228,543,505

Uncovered: 21,992,703 out of 22,421,425
Matches: 241,312 out of 22,421,425
Mismatches: 174,578 out of 22,421,425
Insertions: 12,832 out of 22,421,425
Identity over aligned base-pairs: 56.3%

Block size distribution

Size range All 2,944 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
6.0 bp
10 bp - 100 bp
1,172
94.0 kb
1,076
86.7 kb
100 bp - 1 kb
1,631
524.0 kb
1,221
402.9 kb
1 kb - 10 kb
137
198.9 kb
214
327.4 kb
10 kb - 100 kb
2
38.5 kb
2
38.5 kb