Guillardia theta CCMP2712 vs Phytophthora parasitica Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) 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 parasitica
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 9,279 alignment blocks

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

Uncovered: 86,164,208 out of 87,266,873
Covered: 1,102,665 out of 87,266,873

Uncovered: 29,594,312 out of 30,644,092
Matches: 706,032 out of 30,644,092
Mismatches: 343,011 out of 30,644,092
Insertions: 737 out of 30,644,092
Identity over aligned base-pairs: 67.3%

Phytophthora parasitica

Uncovered: 54,380,693 out of 55,229,644
Covered: 848,951 out of 55,229,644

Uncovered: 26,763,981 out of 27,601,672
Matches: 561,882 out of 27,601,672
Mismatches: 275,623 out of 27,601,672
Insertions: 186 out of 27,601,672
Identity over aligned base-pairs: 67.1%