Guillardia theta CCMP2712 vs Phytophthora ramorum Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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. Guillardia theta CCMP2712 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

ParameterGuillardia theta CCMP2712Phytophthora ramorum
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 9,619 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Guillardia theta CCMP2712

Uncovered: 86,153,831 out of 87,266,873
Covered: 1,113,042 out of 87,266,873

Uncovered: 29,581,951 out of 30,644,092
Matches: 721,324 out of 30,644,092
Mismatches: 340,012 out of 30,644,092
Insertions: 805 out of 30,644,092
Identity over aligned base-pairs: 67.9%

Phytophthora ramorum

Uncovered: 65,790,808 out of 66,652,401
Covered: 861,593 out of 66,652,401

Uncovered: 21,545,412 out of 22,377,278
Matches: 564,082 out of 22,377,278
Mismatches: 267,544 out of 22,377,278
Insertions: 240 out of 22,377,278
Identity over aligned base-pairs: 67.8%