Emiliania huxleyi vs Giardia lamblia Translated Blat results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) 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 74. Emiliania huxleyi 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

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

ParameterEmiliania huxleyiGiardia lamblia
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,956 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Emiliania huxleyi

Uncovered: 167,349,727 out of 167,675,649
Covered: 325,922 out of 167,675,649

Uncovered: 39,446,090 out of 39,740,234
Matches: 201,538 out of 39,740,234
Mismatches: 92,578 out of 39,740,234
Insertions: 28 out of 39,740,234
Identity over aligned base-pairs: 68.5%

Giardia lamblia

Uncovered: 11,052,612 out of 11,192,215
Covered: 139,603 out of 11,192,215

Uncovered: 9,186,336 out of 9,322,001
Matches: 89,967 out of 9,322,001
Mismatches: 45,677 out of 9,322,001
Insertions: 21 out of 9,322,001
Identity over aligned base-pairs: 66.3%