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Entamoeba histolytica vs Giardia lamblia LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Giardia lamblia (Giardia lamblia, GL2) 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 histolyticaGiardia lamblia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 747 alignment blocks

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

Uncovered: 20,509,633 out of 20,835,395
Covered: 325,762 out of 20,835,395

Uncovered: 9,926,348 out of 10,244,611
Matches: 182,041 out of 10,244,611
Mismatches: 129,300 out of 10,244,611
Insertions: 6,922 out of 10,244,611
Identity over aligned base-pairs: 57.2%

Giardia lamblia

Uncovered: 10,992,207 out of 11,192,215
Covered: 200,008 out of 11,192,215

Uncovered: 9,123,661 out of 9,322,001
Matches: 111,213 out of 9,322,001
Mismatches: 79,171 out of 9,322,001
Insertions: 7,956 out of 9,322,001
Identity over aligned base-pairs: 56.1%

Block size distribution

Size range All 747 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
10 bp - 100 bp
43
3.4 kb
22
1.7 kb
100 bp - 1 kb
636
264.7 kb
388
182.2 kb
1 kb - 10 kb
68
96.0 kb
117
180.2 kb