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Zebrafish vs Platyfish Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and Platyfish (Xiphophorus maculatus, Xipmac4.4.2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 69. Zebrafish 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

Zebrafish Platyfish
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: 305,782

Genome coverage (bp) Coding exon coverage (bp)
Danio rerio

Uncovered: 1,379,402,898 out of 1,412,464,843
Covered: 33,061,945 out of 1,412,464,843

Uncovered: 17,937,778 out of 42,417,757
Matches: 18,388,592 out of 42,417,757
Mismatches: 6,079,749 out of 42,417,757
Insertions: 11,638 out of 42,417,757

Xiphophorus maculatus

Uncovered: 703,132,598 out of 729,662,853
Covered: 26,530,255 out of 729,662,853

Uncovered: 13,353,844 out of 33,480,785
Matches: 15,182,617 out of 33,480,785
Mismatches: 4,929,013 out of 33,480,785
Insertions: 15,311 out of 33,480,785