Pythium arrhenomanes vs Pythium ultimum Translated Blat results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) 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 ultimum
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 61,871 alignment blocks

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

Uncovered: 34,095,477 out of 44,672,625
Covered: 10,577,148 out of 44,672,625

Uncovered: 9,359,279 out of 18,367,184
Matches: 6,608,133 out of 18,367,184
Mismatches: 2,394,983 out of 18,367,184
Insertions: 4,789 out of 18,367,184
Identity over aligned base-pairs: 73.4%

Pythium ultimum

Uncovered: 35,174,188 out of 44,913,582
Covered: 9,739,394 out of 44,913,582

Uncovered: 11,264,676 out of 19,826,256
Matches: 6,299,382 out of 19,826,256
Mismatches: 2,258,293 out of 19,826,256
Insertions: 3,905 out of 19,826,256
Identity over aligned base-pairs: 73.6%