Pythium aphanidermatum vs Entamoeba histolytica Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_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 74. Pythium aphanidermatum was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 1,563

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum DAOM BR444

Uncovered: 35,614,399 out of 35,876,849
Covered: 262,450 out of 35,876,849

Uncovered: 17,776,363 out of 18,015,574
Matches: 144,231 out of 18,015,574
Mismatches: 94,892 out of 18,015,574
Insertions: 88 out of 18,015,574

Entamoeba histolytica

Uncovered: 20,629,708 out of 20,835,395
Covered: 205,687 out of 20,835,395

Uncovered: 10,042,540 out of 10,244,611
Matches: 121,406 out of 10,244,611
Mismatches: 80,635 out of 10,244,611
Insertions: 30 out of 10,244,611

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

Pythium aphanidermatum Entamoeba histolytica
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}