Tetrahymena thermophila vs Pythium ultimum Translated Blat Results

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Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Tetrahymena thermophila 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: 4,733

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,395,528 out of 103,014,375
Covered: 618,847 out of 103,014,375

Uncovered: 47,609,816 out of 48,193,658
Matches: 367,615 out of 48,193,658
Mismatches: 216,145 out of 48,193,658
Insertions: 82 out of 48,193,658

Pythium ultimum DAOM BR144

Uncovered: 44,482,068 out of 44,913,582
Covered: 431,514 out of 44,913,582

Uncovered: 19,443,219 out of 19,826,256
Matches: 239,316 out of 19,826,256
Mismatches: 143,697 out of 19,826,256
Insertions: 24 out of 19,826,256

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

Tetrahymena thermophila Pythium ultimum
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}