Guillardia theta CCMP2712 vs Phytophthora lateralis Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis
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 8,004 alignment blocks

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

Uncovered: 86,349,394 out of 87,266,873
Covered: 917,479 out of 87,266,873

Uncovered: 29,770,588 out of 30,644,092
Matches: 588,771 out of 30,644,092
Mismatches: 284,150 out of 30,644,092
Insertions: 583 out of 30,644,092
Identity over aligned base-pairs: 67.4%

Phytophthora lateralis

Uncovered: 43,305,162 out of 43,981,379
Covered: 676,217 out of 43,981,379

Uncovered: 14,054,067 out of 14,663,433
Matches: 409,985 out of 14,663,433
Mismatches: 199,245 out of 14,663,433
Insertions: 136 out of 14,663,433
Identity over aligned base-pairs: 67.3%