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Giardia lamblia vs Emiliania huxleyi LastZ results

Giardia lamblia (Giardia lamblia, GL2) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) 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 lambliaEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,507 alignment blocks

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

Uncovered: 10,898,791 out of 11,192,215
Covered: 293,424 out of 11,192,215

Uncovered: 9,039,903 out of 9,322,001
Matches: 168,255 out of 9,322,001
Mismatches: 103,079 out of 9,322,001
Insertions: 10,764 out of 9,322,001
Identity over aligned base-pairs: 59.6%

Emiliania huxleyi

Uncovered: 167,084,349 out of 167,675,649
Covered: 591,300 out of 167,675,649

Uncovered: 39,223,545 out of 39,740,234
Matches: 323,507 out of 39,740,234
Mismatches: 175,784 out of 39,740,234
Insertions: 17,398 out of 39,740,234
Identity over aligned base-pairs: 62.6%

Block size distribution

Size range All 2,507 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
84.0 bp
10 bp - 100 bp
586
42.1 kb
185
13.5 kb
100 bp - 1 kb
1,834
561.2 kb
1,028
402.3 kb
1 kb - 10 kb
75
97.1 kb
182
284.6 kb