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Emiliania huxleyi vs Phytophthora lateralis LastZ results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 15,484 alignment blocks

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

Uncovered: 164,088,683 out of 167,675,649
Covered: 3,586,966 out of 167,675,649

Uncovered: 36,952,477 out of 39,740,234
Matches: 1,746,727 out of 39,740,234
Mismatches: 897,136 out of 39,740,234
Insertions: 143,894 out of 39,740,234
Identity over aligned base-pairs: 62.7%

Phytophthora lateralis

Uncovered: 41,765,539 out of 43,981,379
Covered: 2,215,840 out of 43,981,379

Uncovered: 12,360,693 out of 14,242,768
Matches: 1,131,897 out of 14,242,768
Mismatches: 665,132 out of 14,242,768
Insertions: 85,046 out of 14,242,768
Identity over aligned base-pairs: 60.1%

Block size distribution

Size range All 15,484 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
89
482.0 bp
10 bp - 100 bp
3,474
237.1 kb
868
60.5 kb
100 bp - 1 kb
11,425
3.5 Mb
5,990
2.3 Mb
1 kb - 10 kb
495
756.1 kb
1,205
2.1 Mb
10 kb - 100 kb
1
25.5 kb
1
25.5 kb