Phytophthora lateralis vs Pythium aphanidermatum Translated Blat Results

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Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis 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: 52,761

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis MPF4

Uncovered: 34,687,162 out of 43,981,379
Covered: 9,294,217 out of 43,981,379

Uncovered: 7,996,734 out of 14,663,433
Matches: 4,757,744 out of 14,663,433
Mismatches: 1,906,420 out of 14,663,433
Insertions: 2,535 out of 14,663,433

Pythium aphanidermatum DAOM BR444

Uncovered: 28,425,974 out of 35,876,849
Covered: 7,450,875 out of 35,876,849

Uncovered: 11,478,447 out of 18,015,574
Matches: 4,646,823 out of 18,015,574
Mismatches: 1,887,682 out of 18,015,574
Insertions: 2,622 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 lateralis 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}