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Emiliania huxleyi vs Phytophthora infestans Translated Blat Results

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Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Emiliania huxleyi was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 14,628

Genome coverage (bp) Coding exon coverage (bp)
Emiliania huxleyi CCMP1516

Uncovered: 166,089,703 out of 167,675,649
Covered: 1,585,946 out of 167,675,649

Uncovered: 38,320,512 out of 39,740,234
Matches: 986,800 out of 39,740,234
Mismatches: 432,700 out of 39,740,234
Insertions: 222 out of 39,740,234

Phytophthora infestans T30-4

Uncovered: 227,656,755 out of 228,543,505
Covered: 886,750 out of 228,543,505

Uncovered: 21,575,048 out of 22,421,425
Matches: 582,098 out of 22,421,425
Mismatches: 264,150 out of 22,421,425
Insertions: 129 out of 22,421,425

Configuration parameters

ParameterValue
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

Emiliania huxleyi Phytophthora infestans
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}