Guillardia theta CCMP2712 vs Bigelowiella natans Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) 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 CCMP2712Bigelowiella natans
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 8,321 alignment blocks

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

Uncovered: 86,441,369 out of 87,266,873
Covered: 825,504 out of 87,266,873

Uncovered: 29,854,460 out of 30,644,092
Matches: 536,255 out of 30,644,092
Mismatches: 253,059 out of 30,644,092
Insertions: 318 out of 30,644,092
Identity over aligned base-pairs: 67.9%

Bigelowiella natans

Uncovered: 94,070,617 out of 94,701,163
Covered: 630,546 out of 94,701,163

Uncovered: 28,214,045 out of 28,817,508
Matches: 409,703 out of 28,817,508
Mismatches: 193,676 out of 28,817,508
Insertions: 84 out of 28,817,508
Identity over aligned base-pairs: 67.9%