Emiliania huxleyi vs Entamoeba histolytica Translated Blat results

Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) 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 huxleyiEntamoeba histolytica
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 1,272 alignment blocks

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

Uncovered: 167,479,986 out of 167,675,649
Covered: 195,663 out of 167,675,649

Uncovered: 39,590,075 out of 39,740,234
Matches: 90,544 out of 39,740,234
Mismatches: 59,609 out of 39,740,234
Insertions: 6 out of 39,740,234
Identity over aligned base-pairs: 60.3%

Entamoeba histolytica

Uncovered: 20,756,372 out of 20,835,395
Covered: 79,023 out of 20,835,395

Uncovered: 10,170,469 out of 10,244,611
Matches: 43,619 out of 10,244,611
Mismatches: 30,517 out of 10,244,611
Insertions: 6 out of 10,244,611
Identity over aligned base-pairs: 58.8%