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Human vs Fugu Translated Blat alignments

Human (Homo sapiens, GRCh37) and Fugu (Takifugu rubripes, FUGU4) 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 Fugu
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: 187,664

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

Uncovered: 3,078,311,920 out of 3,098,825,702
Covered: 20,513,782 out of 3,098,825,702

Uncovered: 20,352,504 out of 35,313,516
Matches: 10,903,429 out of 35,313,516
Mismatches: 4,052,524 out of 35,313,516
Insertions: 5,059 out of 35,313,516

Takifugu rubripes

Uncovered: 378,424,002 out of 393,312,790
Covered: 14,888,788 out of 393,312,790

Uncovered: 21,009,142 out of 33,921,072
Matches: 9,409,568 out of 33,921,072
Mismatches: 3,497,396 out of 33,921,072
Insertions: 4,966 out of 33,921,072