Phytophthora kernoviae vs Pythium iwayamai Translated Blat results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae 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 kernoviaePythium 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 60,885 alignment blocks

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

Uncovered: 32,328,387 out of 43,208,681
Covered: 10,880,294 out of 43,208,681

Uncovered: 5,205,577 out of 11,508,642
Matches: 4,612,303 out of 11,508,642
Mismatches: 1,687,839 out of 11,508,642
Insertions: 2,923 out of 11,508,642
Identity over aligned base-pairs: 73.2%

Pythium iwayamai

Uncovered: 33,765,999 out of 43,199,174
Covered: 9,433,175 out of 43,199,174

Uncovered: 11,057,434 out of 19,552,457
Matches: 6,079,812 out of 19,552,457
Mismatches: 2,412,253 out of 19,552,457
Insertions: 2,958 out of 19,552,457
Identity over aligned base-pairs: 71.6%