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Chicken vs Zebrafish Translated Blat alignments

Chicken (Gallus gallus, Galgal4) 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 71. Chicken 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

Chicken 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: 148,985

Genome coverage (bp) Coding exon coverage (bp)
Gallus gallus

Uncovered: 1,029,875,946 out of 1,046,932,099
Covered: 17,056,153 out of 1,046,932,099

Uncovered: 12,077,708 out of 25,934,237
Matches: 10,085,338 out of 25,934,237
Mismatches: 3,766,888 out of 25,934,237
Insertions: 4,303 out of 25,934,237

Danio rerio

Uncovered: 1,396,935,852 out of 1,412,464,843
Covered: 15,528,991 out of 1,412,464,843

Uncovered: 29,418,457 out of 42,566,667
Matches: 9,577,265 out of 42,566,667
Mismatches: 3,566,326 out of 42,566,667
Insertions: 4,619 out of 42,566,667