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Giardia lamblia vs Guillardia theta CCMP2712 LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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 lambliaGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,611 alignment blocks

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

Uncovered: 10,843,601 out of 11,192,215
Covered: 348,614 out of 11,192,215

Uncovered: 8,981,274 out of 9,322,001
Matches: 201,401 out of 9,322,001
Mismatches: 123,405 out of 9,322,001
Insertions: 15,921 out of 9,322,001
Identity over aligned base-pairs: 59.1%

Guillardia theta CCMP2712

Uncovered: 86,717,586 out of 87,266,873
Covered: 549,287 out of 87,266,873

Uncovered: 30,125,410 out of 30,644,092
Matches: 308,365 out of 30,644,092
Mismatches: 190,856 out of 30,644,092
Insertions: 19,461 out of 30,644,092
Identity over aligned base-pairs: 59.5%

Block size distribution

Size range All 1,611 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
32.0 bp
10 bp - 100 bp
319
22.7 kb
83
6.2 kb
100 bp - 1 kb
1,132
395.0 kb
625
268.6 kb
1 kb - 10 kb
153
238.7 kb
156
371.5 kb
10 kb - 100 kb
1
10.1 kb