Pythium arrhenomanes vs Pythium aphanidermatum Translated Blat results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes 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 arrhenomanesPythium 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 78,817 alignment blocks

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

Uncovered: 29,804,880 out of 44,672,625
Covered: 14,867,745 out of 44,672,625

Uncovered: 6,478,696 out of 18,367,184
Matches: 8,793,584 out of 18,367,184
Mismatches: 3,084,198 out of 18,367,184
Insertions: 10,706 out of 18,367,184
Identity over aligned base-pairs: 74.0%

Pythium aphanidermatum

Uncovered: 22,424,438 out of 35,876,849
Covered: 13,452,411 out of 35,876,849

Uncovered: 6,816,513 out of 18,015,574
Matches: 8,342,109 out of 18,015,574
Mismatches: 2,850,546 out of 18,015,574
Insertions: 6,406 out of 18,015,574
Identity over aligned base-pairs: 74.5%