Phytophthora infestans vs Entamoeba histolytica Translated Blat results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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. Phytophthora infestans 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 infestansEntamoeba 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 2,467 alignment blocks

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

Uncovered: 228,210,410 out of 228,543,505
Covered: 333,095 out of 228,543,505

Uncovered: 22,148,357 out of 22,421,425
Matches: 164,319 out of 22,421,425
Mismatches: 108,710 out of 22,421,425
Insertions: 39 out of 22,421,425
Identity over aligned base-pairs: 60.2%

Entamoeba histolytica

Uncovered: 20,625,515 out of 20,835,395
Covered: 209,880 out of 20,835,395

Uncovered: 10,039,627 out of 10,244,611
Matches: 122,828 out of 10,244,611
Mismatches: 82,143 out of 10,244,611
Insertions: 13 out of 10,244,611
Identity over aligned base-pairs: 59.9%