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Human vs Tetraodon Translated Blat alignments

Human (Homo sapiens, GRCh37) and Tetraodon (Tetraodon nigroviridis, TETRAODON8) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 55. Human 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.

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

Human Tetraodon
Chunk size 1,000,000 25,000
Overlap 10,000 10,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1}

Results

Number of alignment blocks: 192,216

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 3,077,549,386 out of 3,098,825,702
Covered: 21,276,316 out of 3,098,825,702

Uncovered: 20,634,838 out of 35,313,516
Matches: 10,718,439 out of 35,313,516
Mismatches: 3,954,985 out of 35,313,516
Insertions: 5,254 out of 35,313,516

Tetraodon nigroviridis

Uncovered: 344,139,143 out of 358,618,246
Covered: 14,479,103 out of 358,618,246

Uncovered: 17,901,203 out of 30,080,167
Matches: 8,892,990 out of 30,080,167
Mismatches: 3,281,312 out of 30,080,167
Insertions: 4,662 out of 30,080,167