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Emiliania huxleyi vs Giardia intestinalis - GCA_000002435.2 LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Emiliania huxleyi 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

ParameterEmiliania huxleyiGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,497 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Emiliania huxleyi

Uncovered: 167,079,007 out of 167,675,649
Covered: 596,642 out of 167,675,649

Uncovered: 39,219,067 out of 39,740,234
Matches: 326,390 out of 39,740,234
Mismatches: 177,311 out of 39,740,234
Insertions: 17,466 out of 39,740,234
Identity over aligned base-pairs: 62.6%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,780,964 out of 12,078,186
Covered: 297,222 out of 12,078,186

Uncovered: 9,180,311 out of 9,469,365
Matches: 172,278 out of 9,469,365
Mismatches: 105,750 out of 9,469,365
Insertions: 11,026 out of 9,469,365
Identity over aligned base-pairs: 59.6%

Block size distribution

Size range All 2,497 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
584
41.9 kb
181
13.1 kb
100 bp - 1 kb
1,824
559.0 kb
1,014
396.7 kb
1 kb - 10 kb
77
102.4 kb
187
293.6 kb