Pythium iwayamai vs Tetrahymena thermophila Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 iwayamaiTetrahymena thermophila
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 2,581 alignment blocks

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

Uncovered: 42,822,617 out of 43,199,174
Covered: 376,557 out of 43,199,174

Uncovered: 19,212,113 out of 19,552,457
Matches: 210,238 out of 19,552,457
Mismatches: 130,067 out of 19,552,457
Insertions: 39 out of 19,552,457
Identity over aligned base-pairs: 61.8%

Tetrahymena thermophila

Uncovered: 102,700,660 out of 103,014,375
Covered: 313,715 out of 103,014,375

Uncovered: 47,888,208 out of 48,193,658
Matches: 188,243 out of 48,193,658
Mismatches: 117,185 out of 48,193,658
Insertions: 22 out of 48,193,658
Identity over aligned base-pairs: 61.6%