Pythium vexans vs Phytophthora infestans Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_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 75. Pythium vexans was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

ParameterPythium vexansPhytophthora infestans
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 60,533 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium vexans

Uncovered: 22,450,006 out of 33,844,883
Covered: 11,394,877 out of 33,844,883

Uncovered: 8,592,337 out of 18,608,353
Matches: 7,228,797 out of 18,608,353
Mismatches: 2,781,964 out of 18,608,353
Insertions: 5,255 out of 18,608,353
Identity over aligned base-pairs: 72.2%

Phytophthora infestans

Uncovered: 218,085,460 out of 228,543,505
Covered: 10,458,045 out of 228,543,505

Uncovered: 12,854,490 out of 22,421,425
Matches: 6,927,250 out of 22,421,425
Mismatches: 2,635,366 out of 22,421,425
Insertions: 4,319 out of 22,421,425
Identity over aligned base-pairs: 72.4%