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Emiliania huxleyi vs Phytophthora kernoviae LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 huxleyiPhytophthora kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 14,920 alignment blocks

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

Uncovered: 164,472,909 out of 167,675,649
Covered: 3,202,740 out of 167,675,649

Uncovered: 37,121,131 out of 39,740,234
Matches: 1,634,966 out of 39,740,234
Mismatches: 876,852 out of 39,740,234
Insertions: 107,285 out of 39,740,234
Identity over aligned base-pairs: 62.4%

Phytophthora kernoviae

Uncovered: 40,992,550 out of 43,208,681
Covered: 2,216,131 out of 43,208,681

Uncovered: 9,757,078 out of 11,344,308
Matches: 965,709 out of 11,344,308
Mismatches: 565,744 out of 11,344,308
Insertions: 55,777 out of 11,344,308
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 14,920 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
83
467.0 bp
10 bp - 100 bp
3,543
247.3 kb
706
51.0 kb
100 bp - 1 kb
10,869
3.1 Mb
5,289
2.1 Mb
1 kb - 10 kb
423
643.1 kb
1,118
1.9 Mb
10 kb - 100 kb
2
50.2 kb
2
50.2 kb