Guillardia theta CCMP2712 vs Phytophthora kernoviae Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae
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 9,182 alignment blocks

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

Uncovered: 86,165,015 out of 87,266,873
Covered: 1,101,858 out of 87,266,873

Uncovered: 29,589,332 out of 30,644,092
Matches: 706,176 out of 30,644,092
Mismatches: 347,829 out of 30,644,092
Insertions: 755 out of 30,644,092
Identity over aligned base-pairs: 67.0%

Phytophthora kernoviae

Uncovered: 42,349,930 out of 43,208,681
Covered: 858,751 out of 43,208,681

Uncovered: 10,844,718 out of 11,508,642
Matches: 447,348 out of 11,508,642
Mismatches: 216,459 out of 11,508,642
Insertions: 117 out of 11,508,642
Identity over aligned base-pairs: 67.4%