Pythium arrhenomanes vs Phytophthora infestans Translated Blat results

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 75. Pythium arrhenomanes was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

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

ParameterPythium arrhenomanesPhytophthora infestans
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 53,900 alignment blocks

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

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
Identity over aligned base-pairs: 70.7%

Phytophthora infestans

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
Identity over aligned base-pairs: 71.0%