Phytophthora parasitica vs Entamoeba histolytica Translated Blat results

Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) 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 76. Phytophthora parasitica 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

ParameterPhytophthora parasiticaEntamoeba 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 1,627 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora parasitica

Uncovered: 54,960,117 out of 55,229,644
Covered: 269,527 out of 55,229,644

Uncovered: 27,336,056 out of 27,601,672
Matches: 160,190 out of 27,601,672
Mismatches: 105,366 out of 27,601,672
Insertions: 60 out of 27,601,672
Identity over aligned base-pairs: 60.3%

Entamoeba histolytica

Uncovered: 20,626,710 out of 20,835,395
Covered: 208,685 out of 20,835,395

Uncovered: 10,038,711 out of 10,244,611
Matches: 123,610 out of 10,244,611
Mismatches: 82,286 out of 10,244,611
Insertions: 4 out of 10,244,611
Identity over aligned base-pairs: 60.0%