Phaeodactylum tricornutum vs Entamoeba histolytica Translated Blat results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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 70. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumEntamoeba 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 1,600 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 27,323,442 out of 27,568,093
Covered: 244,651 out of 27,568,093

Uncovered: 14,176,783 out of 14,407,044
Matches: 143,456 out of 14,407,044
Mismatches: 86,757 out of 14,407,044
Insertions: 48 out of 14,407,044
Identity over aligned base-pairs: 62.3%

Entamoeba histolytica

Uncovered: 20,633,999 out of 20,835,395
Covered: 201,396 out of 20,835,395

Uncovered: 10,046,192 out of 10,244,611
Matches: 123,311 out of 10,244,611
Mismatches: 75,093 out of 10,244,611
Insertions: 15 out of 10,244,611
Identity over aligned base-pairs: 62.1%