Pythium aphanidermatum vs Emiliania huxleyi Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium aphanidermatum 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: 9,582

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum DAOM BR444

Uncovered: 34,857,838 out of 35,876,849
Covered: 1,019,011 out of 35,876,849

Uncovered: 17,084,752 out of 18,015,574
Matches: 643,815 out of 18,015,574
Mismatches: 286,789 out of 18,015,574
Insertions: 218 out of 18,015,574

Emiliania huxleyi CCMP1516

Uncovered: 166,847,337 out of 167,675,649
Covered: 828,312 out of 167,675,649

Uncovered: 38,983,930 out of 39,740,234
Matches: 523,777 out of 39,740,234
Mismatches: 232,429 out of 39,740,234
Insertions: 98 out of 39,740,234

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

Pythium aphanidermatum Emiliania huxleyi
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}