Pythium aphanidermatum vs Paramecium tetraurelia Translated Blat results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium aphanidermatum 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

ParameterPythium aphanidermatumParamecium tetraurelia
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 3,687 alignment blocks

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

Uncovered: 35,352,475 out of 35,876,849
Covered: 524,374 out of 35,876,849

Uncovered: 17,539,069 out of 18,015,574
Matches: 296,554 out of 18,015,574
Mismatches: 179,897 out of 18,015,574
Insertions: 54 out of 18,015,574
Identity over aligned base-pairs: 62.2%

Paramecium tetraurelia

Uncovered: 71,645,917 out of 72,094,543
Covered: 448,626 out of 72,094,543

Uncovered: 53,602,731 out of 54,045,570
Matches: 275,168 out of 54,045,570
Mismatches: 167,471 out of 54,045,570
Insertions: 200 out of 54,045,570
Identity over aligned base-pairs: 62.1%