Guillardia theta CCMP2712 vs Giardia lamblia Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Giardia lamblia (Giardia lamblia, GL2) 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 CCMP2712Giardia lamblia
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 2,113 alignment blocks

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

Uncovered: 87,014,380 out of 87,266,873
Covered: 252,493 out of 87,266,873

Uncovered: 30,398,342 out of 30,644,092
Matches: 160,568 out of 30,644,092
Mismatches: 85,121 out of 30,644,092
Insertions: 61 out of 30,644,092
Identity over aligned base-pairs: 65.3%

Giardia lamblia

Uncovered: 11,039,281 out of 11,192,215
Covered: 152,934 out of 11,192,215

Uncovered: 9,170,641 out of 9,322,001
Matches: 97,923 out of 9,322,001
Mismatches: 53,432 out of 9,322,001
Insertions: 5 out of 9,322,001
Identity over aligned base-pairs: 64.7%