Pythium iwayamai vs Phytophthora infestans Translated Blat Results

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Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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: 59,282

Genome coverage (bp) Coding exon coverage (bp)
Pythium iwayamai DAOM BR242034

Uncovered: 32,784,188 out of 43,199,174
Covered: 10,414,986 out of 43,199,174

Uncovered: 10,393,799 out of 19,552,457
Matches: 6,571,667 out of 19,552,457
Mismatches: 2,583,560 out of 19,552,457
Insertions: 3,431 out of 19,552,457

Phytophthora infestans T30-4

Uncovered: 219,098,551 out of 228,543,505
Covered: 9,444,954 out of 228,543,505

Uncovered: 13,885,066 out of 22,421,425
Matches: 6,161,617 out of 22,421,425
Mismatches: 2,371,158 out of 22,421,425
Insertions: 3,584 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 iwayamai 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}