Pythium arrhenomanes vs Pythium aphanidermatum Translated Blat Results

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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 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: 78,817

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

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

Pythium aphanidermatum DAOM BR444

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

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 aphanidermatum
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}