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Human vs Tilapia Translated Blat alignments

Human (Homo sapiens, GRCh37) and Tilapia (Oreochromis niloticus, Orenil1.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 67. 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 Tilapia
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: 197,965

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

Uncovered: 3,077,248,227 out of 3,098,825,702
Covered: 21,577,475 out of 3,098,825,702

Uncovered: 19,847,792 out of 35,313,516
Matches: 11,271,950 out of 35,313,516
Mismatches: 4,189,082 out of 35,313,516
Insertions: 4,692 out of 35,313,516

Oreochromis niloticus

Uncovered: 911,120,740 out of 927,383,394
Covered: 16,262,654 out of 927,383,394

Uncovered: 23,438,825 out of 37,304,121
Matches: 10,118,140 out of 37,304,121
Mismatches: 3,740,797 out of 37,304,121
Insertions: 6,359 out of 37,304,121