Phytophthora infestans vs Phytophthora ramorum Translated Blat results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 70. Phytophthora infestans 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

ParameterPhytophthora infestansPhytophthora ramorum
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 185,009 alignment blocks

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

Uncovered: 193,173,229 out of 228,543,505
Covered: 35,370,276 out of 228,543,505

Uncovered: 3,919,873 out of 22,421,425
Matches: 14,503,026 out of 22,421,425
Mismatches: 3,974,416 out of 22,421,425
Insertions: 24,110 out of 22,421,425
Identity over aligned base-pairs: 78.4%

Phytophthora ramorum

Uncovered: 46,179,068 out of 66,652,401
Covered: 20,473,333 out of 66,652,401

Uncovered: 7,396,927 out of 22,377,278
Matches: 11,812,940 out of 22,377,278
Mismatches: 3,135,751 out of 22,377,278
Insertions: 31,660 out of 22,377,278
Identity over aligned base-pairs: 78.9%