Pythium iwayamai vs Pythium aphanidermatum Translated Blat Results

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Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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: 59,049

Genome coverage (bp) Coding exon coverage (bp)
Pythium iwayamai DAOM BR242034

Uncovered: 32,811,768 out of 43,199,174
Covered: 10,387,406 out of 43,199,174

Uncovered: 10,393,272 out of 19,552,457
Matches: 6,641,010 out of 19,552,457
Mismatches: 2,514,282 out of 19,552,457
Insertions: 3,893 out of 19,552,457

Pythium aphanidermatum DAOM BR444

Uncovered: 26,524,688 out of 35,876,849
Covered: 9,352,161 out of 35,876,849

Uncovered: 9,798,955 out of 18,015,574
Matches: 5,994,003 out of 18,015,574
Mismatches: 2,219,326 out of 18,015,574
Insertions: 3,290 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 iwayamai 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}