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Emiliania huxleyi vs Phytophthora parasitica LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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 huxleyiPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 15,837 alignment blocks

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

Uncovered: 164,197,706 out of 167,675,649
Covered: 3,477,943 out of 167,675,649

Uncovered: 36,928,974 out of 39,740,234
Matches: 1,764,228 out of 39,740,234
Mismatches: 925,116 out of 39,740,234
Insertions: 121,916 out of 39,740,234
Identity over aligned base-pairs: 62.8%

Phytophthora parasitica

Uncovered: 52,768,597 out of 55,229,644
Covered: 2,461,047 out of 55,229,644

Uncovered: 25,268,648 out of 27,601,672
Matches: 1,371,935 out of 27,601,672
Mismatches: 874,190 out of 27,601,672
Insertions: 86,899 out of 27,601,672
Identity over aligned base-pairs: 58.8%

Block size distribution

Size range All 15,837 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
85
498.0 bp
10 bp - 100 bp
3,634
252.8 kb
747
53.8 kb
100 bp - 1 kb
11,640
3.5 Mb
5,592
2.3 Mb
1 kb - 10 kb
474
738.8 kb
1,258
2.1 Mb
10 kb - 100 kb
4
82.8 kb
5
116.9 kb