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Entamoeba histolytica vs Bigelowiella natans LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) 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 histolyticaBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,934 alignment blocks

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

Uncovered: 20,300,713 out of 20,835,395
Covered: 534,682 out of 20,835,395

Uncovered: 9,737,662 out of 10,244,611
Matches: 295,640 out of 10,244,611
Mismatches: 199,850 out of 10,244,611
Insertions: 11,459 out of 10,244,611
Identity over aligned base-pairs: 58.3%

Bigelowiella natans

Uncovered: 94,302,287 out of 94,701,163
Covered: 398,876 out of 94,701,163

Uncovered: 28,457,211 out of 28,817,508
Matches: 212,941 out of 28,817,508
Mismatches: 134,269 out of 28,817,508
Insertions: 13,087 out of 28,817,508
Identity over aligned base-pairs: 59.1%

Block size distribution

Size range All 1,934 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
15.0 bp
10 bp - 100 bp
385
27.3 kb
100
7.3 kb
100 bp - 1 kb
1,420
445.8 kb
836
340.4 kb
1 kb - 10 kb
127
205.3 kb
198
330.7 kb