Guillardia theta CCMP2712 vs Tetrahymena thermophila Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 CCMP2712Tetrahymena thermophila
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 3,785 alignment blocks

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

Uncovered: 86,820,327 out of 87,266,873
Covered: 446,546 out of 87,266,873

Uncovered: 30,212,098 out of 30,644,092
Matches: 278,153 out of 30,644,092
Mismatches: 153,625 out of 30,644,092
Insertions: 216 out of 30,644,092
Identity over aligned base-pairs: 64.4%

Tetrahymena thermophila

Uncovered: 102,677,957 out of 103,014,375
Covered: 336,418 out of 103,014,375

Uncovered: 47,867,213 out of 48,193,658
Matches: 209,141 out of 48,193,658
Mismatches: 117,271 out of 48,193,658
Insertions: 33 out of 48,193,658
Identity over aligned base-pairs: 64.1%