Phytophthora parasitica vs Pythium iwayamai Translated Blat results

Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) 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 parasitica 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 parasiticaPythium 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 73,943 alignment blocks

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

Uncovered: 42,456,524 out of 55,229,644
Covered: 12,773,120 out of 55,229,644

Uncovered: 16,415,911 out of 27,601,672
Matches: 7,986,356 out of 27,601,672
Mismatches: 3,194,568 out of 27,601,672
Insertions: 4,837 out of 27,601,672
Identity over aligned base-pairs: 71.4%

Pythium iwayamai

Uncovered: 33,467,402 out of 43,199,174
Covered: 9,731,772 out of 43,199,174

Uncovered: 10,892,100 out of 19,552,457
Matches: 6,223,653 out of 19,552,457
Mismatches: 2,433,182 out of 19,552,457
Insertions: 3,522 out of 19,552,457
Identity over aligned base-pairs: 71.9%