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Emiliania huxleyi vs Pythium vexans LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) 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 huxleyiPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 25,238 alignment blocks

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

Uncovered: 161,189,320 out of 167,675,649
Covered: 6,486,329 out of 167,675,649

Uncovered: 35,243,924 out of 39,740,234
Matches: 2,808,350 out of 39,740,234
Mismatches: 1,400,077 out of 39,740,234
Insertions: 287,883 out of 39,740,234
Identity over aligned base-pairs: 62.5%

Pythium vexans

Uncovered: 30,006,606 out of 33,844,883
Covered: 3,838,277 out of 33,844,883

Uncovered: 15,420,305 out of 18,608,353
Matches: 1,926,816 out of 18,608,353
Mismatches: 1,074,288 out of 18,608,353
Insertions: 186,944 out of 18,608,353
Identity over aligned base-pairs: 60.4%

Block size distribution

Size range All 25,238 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
112
605.0 bp
10 bp - 100 bp
6,000
404.0 kb
2,267
150.4 kb
100 bp - 1 kb
17,786
5.8 Mb
9,357
3.9 Mb
1 kb - 10 kb
1,339
2.1 Mb
2,468
4.3 Mb
10 kb - 100 kb
1
14.9 kb
2
33.5 kb