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Entamoeba histolytica vs Guillardia theta CCMP2712 LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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 histolyticaGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,548 alignment blocks

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

Uncovered: 20,371,399 out of 20,835,395
Covered: 463,996 out of 20,835,395

Uncovered: 9,797,411 out of 10,244,611
Matches: 264,882 out of 10,244,611
Mismatches: 174,400 out of 10,244,611
Insertions: 7,918 out of 10,244,611
Identity over aligned base-pairs: 59.2%

Guillardia theta CCMP2712

Uncovered: 86,915,745 out of 87,266,873
Covered: 351,128 out of 87,266,873

Uncovered: 30,321,922 out of 30,644,092
Matches: 186,490 out of 30,644,092
Mismatches: 124,574 out of 30,644,092
Insertions: 11,106 out of 30,644,092
Identity over aligned base-pairs: 57.9%

Block size distribution

Size range All 1,548 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
13.0 bp
10 bp - 100 bp
257
17.7 kb
65
4.8 kb
100 bp - 1 kb
1,188
434.4 kb
704
306.4 kb
1 kb - 10 kb
101
146.0 kb
185
286.9 kb