Bigelowiella natans vs Giardia lamblia Translated Blat results

Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) 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 75. Bigelowiella natans 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

ParameterBigelowiella natansGiardia 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 1,610 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Bigelowiella natans

Uncovered: 94,511,012 out of 94,701,163
Covered: 190,151 out of 94,701,163

Uncovered: 28,632,988 out of 28,817,508
Matches: 120,218 out of 28,817,508
Mismatches: 64,293 out of 28,817,508
Insertions: 9 out of 28,817,508
Identity over aligned base-pairs: 65.2%

Giardia lamblia

Uncovered: 11,071,047 out of 11,192,215
Covered: 121,168 out of 11,192,215

Uncovered: 9,201,352 out of 9,322,001
Matches: 77,545 out of 9,322,001
Mismatches: 43,047 out of 9,322,001
Insertions: 57 out of 9,322,001
Identity over aligned base-pairs: 64.3%