Phytophthora parasitica vs Pythium aphanidermatum Translated Blat Results

Back to all analyses

Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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. Phytophthora parasitica 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: 64,673

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora parasitica P1569

Uncovered: 43,507,360 out of 55,229,644
Covered: 11,722,284 out of 55,229,644

Uncovered: 17,212,618 out of 27,601,672
Matches: 7,290,387 out of 27,601,672
Mismatches: 3,094,601 out of 27,601,672
Insertions: 4,066 out of 27,601,672

Pythium aphanidermatum DAOM BR444

Uncovered: 26,788,277 out of 35,876,849
Covered: 9,088,572 out of 35,876,849

Uncovered: 10,023,420 out of 18,015,574
Matches: 5,650,375 out of 18,015,574
Mismatches: 2,338,858 out of 18,015,574
Insertions: 2,921 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

Phytophthora parasitica 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}