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Emiliania huxleyi vs Guillardia theta CCMP2712 LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 huxleyiGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 18,391 alignment blocks

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

Uncovered: 163,815,191 out of 167,675,649
Covered: 3,860,458 out of 167,675,649

Uncovered: 36,857,909 out of 39,740,234
Matches: 1,824,613 out of 39,740,234
Mismatches: 928,334 out of 39,740,234
Insertions: 129,378 out of 39,740,234
Identity over aligned base-pairs: 63.3%

Guillardia theta CCMP2712

Uncovered: 84,646,014 out of 87,266,873
Covered: 2,620,859 out of 87,266,873

Uncovered: 28,490,524 out of 30,644,092
Matches: 1,294,151 out of 30,644,092
Mismatches: 774,364 out of 30,644,092
Insertions: 85,053 out of 30,644,092
Identity over aligned base-pairs: 60.1%

Block size distribution

Size range All 18,391 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
78
436.0 bp
10 bp - 100 bp
5,366
365.3 kb
1,248
85.3 kb
100 bp - 1 kb
12,427
3.7 Mb
6,357
2.5 Mb
1 kb - 10 kb
513
792.3 kb
1,275
2.2 Mb
10 kb - 100 kb
7
130.1 kb
7
136.3 kb