Pythium aphanidermatum vs Phytophthora infestans Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium aphanidermatum 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: 51,475

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum DAOM BR444

Uncovered: 26,308,853 out of 35,876,849
Covered: 9,567,996 out of 35,876,849

Uncovered: 9,633,753 out of 18,015,574
Matches: 5,910,849 out of 18,015,574
Mismatches: 2,468,168 out of 18,015,574
Insertions: 2,804 out of 18,015,574

Phytophthora infestans T30-4

Uncovered: 219,758,399 out of 228,543,505
Covered: 8,785,106 out of 228,543,505

Uncovered: 14,368,542 out of 22,421,425
Matches: 5,684,565 out of 22,421,425
Mismatches: 2,364,903 out of 22,421,425
Insertions: 3,415 out of 22,421,425

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 aphanidermatum Phytophthora infestans
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}