Phytophthora parasitica vs Phytophthora infestans Translated Blat Results

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Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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. 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: 132,491

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

Uncovered: 23,874,450 out of 55,229,644
Covered: 31,355,194 out of 55,229,644

Uncovered: 4,017,277 out of 27,601,672
Matches: 19,770,057 out of 27,601,672
Mismatches: 3,755,441 out of 27,601,672
Insertions: 58,897 out of 27,601,672

Phytophthora infestans T30-4

Uncovered: 201,325,001 out of 228,543,505
Covered: 27,218,504 out of 228,543,505

Uncovered: 4,777,974 out of 22,421,425
Matches: 15,097,375 out of 22,421,425
Mismatches: 2,516,260 out of 22,421,425
Insertions: 29,816 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

Phytophthora parasitica 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}