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Mouse vs Zebrafish Translated Blat alignments

Mouse (Mus musculus, GRCm38) 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 68. Mouse 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

Mouse 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} {default_soft_masking => 1}

Results

Number of alignment blocks: 197,907

Genome coverage (bp) Coding exon coverage (bp)
Mus musculus

Uncovered: 2,709,418,760 out of 2,730,871,774
Covered: 21,453,014 out of 2,730,871,774

Uncovered: 20,436,203 out of 35,991,038
Matches: 11,290,260 out of 35,991,038
Mismatches: 4,259,180 out of 35,991,038
Insertions: 5,395 out of 35,991,038

Danio rerio

Uncovered: 1,396,422,272 out of 1,412,464,843
Covered: 16,042,571 out of 1,412,464,843

Uncovered: 28,798,280 out of 42,417,757
Matches: 9,900,707 out of 42,417,757
Mismatches: 3,714,026 out of 42,417,757
Insertions: 4,744 out of 42,417,757