Pythium aphanidermatum vs Tetrahymena thermophila Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 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: 3,918

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

Uncovered: 35,349,195 out of 35,876,849
Covered: 527,654 out of 35,876,849

Uncovered: 17,529,083 out of 18,015,574
Matches: 308,187 out of 18,015,574
Mismatches: 178,238 out of 18,015,574
Insertions: 66 out of 18,015,574

Tetrahymena thermophila

Uncovered: 102,576,256 out of 103,014,375
Covered: 438,119 out of 103,014,375

Uncovered: 47,764,666 out of 48,193,658
Matches: 271,212 out of 48,193,658
Mismatches: 157,746 out of 48,193,658
Insertions: 34 out of 48,193,658

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 Tetrahymena thermophila
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}