Pythium arrhenomanes vs Pythium ultimum Translated Blat Results

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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 74. Pythium arrhenomanes was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 61,871

Genome coverage (bp) Coding exon coverage (bp)
Pythium arrhenomanes ATCC 12531

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

Pythium ultimum DAOM BR144

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

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

Pythium arrhenomanes Pythium ultimum
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}