Pythium iwayamai vs Phytophthora infestans Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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 iwayamaiPhytophthora 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 59,282 alignment blocks

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

Uncovered: 32,784,188 out of 43,199,174
Covered: 10,414,986 out of 43,199,174

Uncovered: 10,393,799 out of 19,552,457
Matches: 6,571,667 out of 19,552,457
Mismatches: 2,583,560 out of 19,552,457
Insertions: 3,431 out of 19,552,457
Identity over aligned base-pairs: 71.8%

Phytophthora infestans

Uncovered: 219,098,551 out of 228,543,505
Covered: 9,444,954 out of 228,543,505

Uncovered: 13,885,066 out of 22,421,425
Matches: 6,161,617 out of 22,421,425
Mismatches: 2,371,158 out of 22,421,425
Insertions: 3,584 out of 22,421,425
Identity over aligned base-pairs: 72.2%