Pythium arrhenomanes vs Phytophthora infestans Translated Blat Results

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Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) 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. 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: 53,900

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

Uncovered: 35,488,614 out of 44,672,625
Covered: 9,184,011 out of 44,672,625

Uncovered: 10,470,698 out of 18,367,184
Matches: 5,583,082 out of 18,367,184
Mismatches: 2,310,595 out of 18,367,184
Insertions: 2,809 out of 18,367,184

Phytophthora infestans T30-4

Uncovered: 220,102,331 out of 228,543,505
Covered: 8,441,174 out of 228,543,505

Uncovered: 14,757,616 out of 22,421,425
Matches: 5,444,621 out of 22,421,425
Mismatches: 2,216,437 out of 22,421,425
Insertions: 2,751 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

Pythium arrhenomanes 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}