Pythium vexans vs Pythium arrhenomanes Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 vexans 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 vexansPythium arrhenomanes
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 59,610 alignment blocks

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

Uncovered: 24,082,301 out of 33,844,883
Covered: 9,762,582 out of 33,844,883

Uncovered: 9,984,801 out of 18,608,353
Matches: 6,376,983 out of 18,608,353
Mismatches: 2,242,577 out of 18,608,353
Insertions: 3,992 out of 18,608,353
Identity over aligned base-pairs: 73.9%

Pythium arrhenomanes

Uncovered: 35,982,036 out of 44,672,625
Covered: 8,690,589 out of 44,672,625

Uncovered: 10,789,614 out of 18,367,184
Matches: 5,621,751 out of 18,367,184
Mismatches: 1,951,777 out of 18,367,184
Insertions: 4,042 out of 18,367,184
Identity over aligned base-pairs: 74.2%