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Human vs Zebrafish Translated Blat alignments

Human (Homo sapiens, GRCh37) and Zebrafish (Danio rerio, Zv9) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 60. 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 Zebrafish
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: 195,763

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

Uncovered: 3,077,272,588 out of 3,098,825,702
Covered: 21,553,114 out of 3,098,825,702

Uncovered: 19,862,285 out of 35,313,516
Matches: 11,229,691 out of 35,313,516
Mismatches: 4,216,082 out of 35,313,516
Insertions: 5,458 out of 35,313,516

Danio rerio

Uncovered: 1,396,540,551 out of 1,412,464,843
Covered: 15,924,292 out of 1,412,464,843

Uncovered: 29,090,830 out of 42,417,757
Matches: 9,681,339 out of 42,417,757
Mismatches: 3,640,607 out of 42,417,757
Insertions: 4,981 out of 42,417,757