Pythium arrhenomanes vs Emiliania huxleyi Translated Blat Results

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Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes 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: 12,197

Genome coverage (bp) Coding exon coverage (bp)
Pythium arrhenomanes ATCC 12531

Uncovered: 43,536,057 out of 44,672,625
Covered: 1,136,568 out of 44,672,625

Uncovered: 17,375,188 out of 18,367,184
Matches: 710,238 out of 18,367,184
Mismatches: 281,476 out of 18,367,184
Insertions: 282 out of 18,367,184

Emiliania huxleyi CCMP1516

Uncovered: 166,728,160 out of 167,675,649
Covered: 947,489 out of 167,675,649

Uncovered: 38,897,722 out of 39,740,234
Matches: 603,983 out of 39,740,234
Mismatches: 238,407 out of 39,740,234
Insertions: 122 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 arrhenomanes 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}