Guillardia theta CCMP2712 vs Emiliania huxleyi Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) 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 CCMP2712Emiliania huxleyi
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 12,641 alignment blocks

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

Uncovered: 86,089,478 out of 87,266,873
Covered: 1,177,395 out of 87,266,873

Uncovered: 29,541,107 out of 30,644,092
Matches: 769,610 out of 30,644,092
Mismatches: 332,748 out of 30,644,092
Insertions: 627 out of 30,644,092
Identity over aligned base-pairs: 69.8%

Emiliania huxleyi

Uncovered: 166,749,416 out of 167,675,649
Covered: 926,233 out of 167,675,649

Uncovered: 38,916,782 out of 39,740,234
Matches: 573,241 out of 39,740,234
Mismatches: 250,045 out of 39,740,234
Insertions: 166 out of 39,740,234
Identity over aligned base-pairs: 69.6%