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Phytophthora infestans vs Emiliania huxleyi LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora infestans 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

ParameterPhytophthora infestansEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 20,189 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

Uncovered: 224,377,031 out of 228,543,505
Covered: 4,166,474 out of 228,543,505

Uncovered: 20,125,003 out of 22,421,425
Matches: 1,380,437 out of 22,421,425
Mismatches: 828,018 out of 22,421,425
Insertions: 87,967 out of 22,421,425
Identity over aligned base-pairs: 60.1%

Emiliania huxleyi

Uncovered: 163,618,598 out of 167,675,649
Covered: 4,057,051 out of 167,675,649

Uncovered: 36,849,492 out of 39,740,234
Matches: 1,716,501 out of 39,740,234
Mismatches: 1,051,429 out of 39,740,234
Insertions: 122,812 out of 39,740,234
Identity over aligned base-pairs: 59.4%

Block size distribution

Size range All 20,189 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
97
551.0 bp
10 bp - 100 bp
4,916
349.6 kb
1,801
139.6 kb
100 bp - 1 kb
14,416
4.4 Mb
7,826
3.1 Mb
1 kb - 10 kb
728
1.4 Mb
1,457
2.7 Mb
10 kb - 100 kb
32
647.6 kb
45
862.4 kb