Pythium aphanidermatum vs Phytophthora infestans Translated Blat results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum 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

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

ParameterPythium aphanidermatumPhytophthora infestans
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 51,475 alignment blocks

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

Uncovered: 26,308,853 out of 35,876,849
Covered: 9,567,996 out of 35,876,849

Uncovered: 9,633,753 out of 18,015,574
Matches: 5,910,849 out of 18,015,574
Mismatches: 2,468,168 out of 18,015,574
Insertions: 2,804 out of 18,015,574
Identity over aligned base-pairs: 70.5%

Phytophthora infestans

Uncovered: 219,758,399 out of 228,543,505
Covered: 8,785,106 out of 228,543,505

Uncovered: 14,368,542 out of 22,421,425
Matches: 5,684,565 out of 22,421,425
Mismatches: 2,364,903 out of 22,421,425
Insertions: 3,415 out of 22,421,425
Identity over aligned base-pairs: 70.6%