Phytophthora lateralis vs Entamoeba histolytica Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_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 76. Phytophthora lateralis 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 lateralisEntamoeba 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 921 alignment blocks

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

Uncovered: 43,818,504 out of 43,981,379
Covered: 162,875 out of 43,981,379

Uncovered: 14,521,187 out of 14,663,433
Matches: 84,342 out of 14,663,433
Mismatches: 57,892 out of 14,663,433
Insertions: 12 out of 14,663,433
Identity over aligned base-pairs: 59.3%

Entamoeba histolytica

Uncovered: 20,700,395 out of 20,835,395
Covered: 135,000 out of 20,835,395

Uncovered: 10,111,745 out of 10,244,611
Matches: 78,858 out of 10,244,611
Mismatches: 54,002 out of 10,244,611
Insertions: 6 out of 10,244,611
Identity over aligned base-pairs: 59.4%