Emiliania huxleyi vs Phaeodactylum tricornutum Translated Blat results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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

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

ParameterEmiliania huxleyiPhaeodactylum tricornutum
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 13,796 alignment blocks

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

Uncovered: 166,067,086 out of 167,675,649
Covered: 1,608,563 out of 167,675,649

Uncovered: 38,291,241 out of 39,740,234
Matches: 960,929 out of 39,740,234
Mismatches: 487,787 out of 39,740,234
Insertions: 277 out of 39,740,234
Identity over aligned base-pairs: 66.3%

Phaeodactylum tricornutum

Uncovered: 26,688,995 out of 27,568,093
Covered: 879,098 out of 27,568,093

Uncovered: 13,570,820 out of 14,407,044
Matches: 548,779 out of 14,407,044
Mismatches: 287,271 out of 14,407,044
Insertions: 174 out of 14,407,044
Identity over aligned base-pairs: 65.6%