Pythium iwayamai vs Pythium aphanidermatum Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) 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 iwayamaiPythium aphanidermatum
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 59,049 alignment blocks

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

Uncovered: 32,811,768 out of 43,199,174
Covered: 10,387,406 out of 43,199,174

Uncovered: 10,393,272 out of 19,552,457
Matches: 6,641,010 out of 19,552,457
Mismatches: 2,514,282 out of 19,552,457
Insertions: 3,893 out of 19,552,457
Identity over aligned base-pairs: 72.5%

Pythium aphanidermatum

Uncovered: 26,524,688 out of 35,876,849
Covered: 9,352,161 out of 35,876,849

Uncovered: 9,798,955 out of 18,015,574
Matches: 5,994,003 out of 18,015,574
Mismatches: 2,219,326 out of 18,015,574
Insertions: 3,290 out of 18,015,574
Identity over aligned base-pairs: 72.9%