Phytophthora parasitica vs Phytophthora infestans Translated Blat results

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 76. Phytophthora parasitica 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

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

ParameterPhytophthora parasiticaPhytophthora infestans
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 132,491 alignment blocks

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

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
Identity over aligned base-pairs: 83.8%

Phytophthora infestans

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
Identity over aligned base-pairs: 85.6%