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Human vs Cod Translated Blat alignments

Human (Homo sapiens, GRCh37) and Cod (Gadus morhua, gadMor1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 65. 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 Cod
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: 176,221

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

Uncovered: 3,079,183,030 out of 3,098,825,702
Covered: 19,642,672 out of 3,098,825,702

Uncovered: 20,833,866 out of 35,313,516
Matches: 10,610,477 out of 35,313,516
Mismatches: 3,864,640 out of 35,313,516
Insertions: 4,533 out of 35,313,516

Gadus morhua

Uncovered: 818,069,842 out of 832,114,588
Covered: 14,044,746 out of 832,114,588

Uncovered: 17,945,726 out of 29,438,356
Matches: 8,415,929 out of 29,438,356
Mismatches: 3,072,497 out of 29,438,356
Insertions: 4,204 out of 29,438,356