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Giardia lamblia vs Paramecium tetraurelia LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Giardia lamblia 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

ParameterGiardia lambliaParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,493 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Giardia lamblia

Uncovered: 10,888,863 out of 11,192,215
Covered: 303,352 out of 11,192,215

Uncovered: 9,028,381 out of 9,322,001
Matches: 163,896 out of 9,322,001
Mismatches: 117,048 out of 9,322,001
Insertions: 12,676 out of 9,322,001
Identity over aligned base-pairs: 55.8%

Paramecium tetraurelia

Uncovered: 71,043,067 out of 72,094,543
Covered: 1,051,476 out of 72,094,543

Uncovered: 53,045,028 out of 54,044,574
Matches: 572,267 out of 54,044,574
Mismatches: 395,806 out of 54,044,574
Insertions: 31,473 out of 54,044,574
Identity over aligned base-pairs: 57.3%

Block size distribution

Size range All 2,493 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
25.0 bp
10 bp - 100 bp
259
18.4 kb
138
10.7 kb
100 bp - 1 kb
2,014
838.4 kb
1,234
579.4 kb
1 kb - 10 kb
215
290.8 kb
294
557.5 kb