Phytophthora kernoviae vs Phytophthora ramorum Translated Blat results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 76. Phytophthora kernoviae 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 kernoviaePhytophthora 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 77,480 alignment blocks

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

Uncovered: 24,127,391 out of 43,208,681
Covered: 19,081,290 out of 43,208,681

Uncovered: 2,145,924 out of 11,508,642
Matches: 7,400,310 out of 11,508,642
Mismatches: 1,947,638 out of 11,508,642
Insertions: 14,770 out of 11,508,642
Identity over aligned base-pairs: 79.0%

Phytophthora ramorum

Uncovered: 48,646,948 out of 66,652,401
Covered: 18,005,453 out of 66,652,401

Uncovered: 8,273,250 out of 22,377,278
Matches: 10,925,820 out of 22,377,278
Mismatches: 3,163,082 out of 22,377,278
Insertions: 15,126 out of 22,377,278
Identity over aligned base-pairs: 77.5%