Phytophthora lateralis vs Pythium iwayamai Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 76. Phytophthora lateralis 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

ParameterPhytophthora lateralisPythium iwayamai
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 61,267 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis

Uncovered: 33,756,602 out of 43,981,379
Covered: 10,224,777 out of 43,981,379

Uncovered: 7,558,833 out of 14,663,433
Matches: 5,241,601 out of 14,663,433
Mismatches: 1,859,642 out of 14,663,433
Insertions: 3,357 out of 14,663,433
Identity over aligned base-pairs: 73.8%

Pythium iwayamai

Uncovered: 35,055,170 out of 43,199,174
Covered: 8,144,004 out of 43,199,174

Uncovered: 12,343,070 out of 19,552,457
Matches: 5,264,890 out of 19,552,457
Mismatches: 1,940,667 out of 19,552,457
Insertions: 3,830 out of 19,552,457
Identity over aligned base-pairs: 73.0%