Pythium iwayamai vs Paramecium tetraurelia Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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 iwayamaiParamecium 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 2,574 alignment blocks

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

Uncovered: 42,810,879 out of 43,199,174
Covered: 388,295 out of 43,199,174

Uncovered: 19,203,628 out of 19,552,457
Matches: 212,324 out of 19,552,457
Mismatches: 136,484 out of 19,552,457
Insertions: 21 out of 19,552,457
Identity over aligned base-pairs: 60.9%

Paramecium tetraurelia

Uncovered: 71,754,068 out of 72,094,543
Covered: 340,475 out of 72,094,543

Uncovered: 53,709,652 out of 54,045,570
Matches: 204,136 out of 54,045,570
Mismatches: 131,609 out of 54,045,570
Insertions: 173 out of 54,045,570
Identity over aligned base-pairs: 60.8%