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Human vs Medaka Translated Blat alignments

Human (Homo sapiens, GRCh37) and Medaka (Oryzias latipes, MEDAKA1) 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 Medaka
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: 189,355

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

Uncovered: 3,078,306,522 out of 3,098,825,702
Covered: 20,519,180 out of 3,098,825,702

Uncovered: 20,388,166 out of 35,313,516
Matches: 10,868,612 out of 35,313,516
Mismatches: 4,052,107 out of 35,313,516
Insertions: 4,631 out of 35,313,516

Oryzias latipes

Uncovered: 854,080,794 out of 868,983,502
Covered: 14,902,708 out of 868,983,502

Uncovered: 18,237,464 out of 30,193,605
Matches: 8,710,658 out of 30,193,605
Mismatches: 3,240,706 out of 30,193,605
Insertions: 4,777 out of 30,193,605