Pythium iwayamai vs Emiliania huxleyi Translated Blat Results

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Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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: 12,379

Genome coverage (bp) Coding exon coverage (bp)
Pythium iwayamai DAOM BR242034

Uncovered: 42,056,377 out of 43,199,174
Covered: 1,142,797 out of 43,199,174

Uncovered: 18,534,498 out of 19,552,457
Matches: 738,004 out of 19,552,457
Mismatches: 279,705 out of 19,552,457
Insertions: 250 out of 19,552,457

Emiliania huxleyi CCMP1516

Uncovered: 166,741,387 out of 167,675,649
Covered: 934,262 out of 167,675,649

Uncovered: 38,911,743 out of 39,740,234
Matches: 601,520 out of 39,740,234
Mismatches: 226,707 out of 39,740,234
Insertions: 264 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 iwayamai 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}