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Emiliania huxleyi vs Pythium aphanidermatum LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 16,836 alignment blocks

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

Uncovered: 163,750,573 out of 167,675,649
Covered: 3,925,076 out of 167,675,649

Uncovered: 36,677,345 out of 39,740,234
Matches: 1,894,630 out of 39,740,234
Mismatches: 1,025,270 out of 39,740,234
Insertions: 142,989 out of 39,740,234
Identity over aligned base-pairs: 61.9%

Pythium aphanidermatum

Uncovered: 33,315,907 out of 35,876,849
Covered: 2,560,942 out of 35,876,849

Uncovered: 15,850,104 out of 18,015,574
Matches: 1,276,051 out of 18,015,574
Mismatches: 798,009 out of 18,015,574
Insertions: 91,410 out of 18,015,574
Identity over aligned base-pairs: 58.9%

Block size distribution

Size range All 16,836 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
97
486.0 bp
10 bp - 100 bp
3,836
262.9 kb
881
60.0 kb
100 bp - 1 kb
12,310
3.7 Mb
6,070
2.4 Mb
1 kb - 10 kb
587
894.8 kb
1,372
2.4 Mb
10 kb - 100 kb
6
86.1 kb
5
108.2 kb