Pythium irregulare vs Phytophthora infestans Translated Blat Results

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Pythium irregulare (Pythium irregulare DAOM BR486, pir_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 irregulare 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.


Number of alignment blocks: 59,557

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare DAOM BR486

Uncovered: 32,061,539 out of 42,968,084
Covered: 10,906,545 out of 42,968,084

Uncovered: 10,723,511 out of 20,543,058
Matches: 7,042,238 out of 20,543,058
Mismatches: 2,772,231 out of 20,543,058
Insertions: 5,078 out of 20,543,058

Phytophthora infestans T30-4

Uncovered: 218,544,852 out of 228,543,505
Covered: 9,998,653 out of 228,543,505

Uncovered: 13,248,934 out of 22,421,425
Matches: 6,608,145 out of 22,421,425
Mismatches: 2,560,304 out of 22,421,425
Insertions: 4,042 out of 22,421,425

Configuration parameters

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 irregulare 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}