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Zebrafish vs Xenopus Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and Xenopus (Xenopus tropicalis, JGI_4.2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 62. 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 Xenopus
Chunk size 1,000,000 25,000
Overlap 1,000 1,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}

Results

Number of alignment blocks: 191,372

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

Uncovered: 1,389,701,926 out of 1,412,464,843
Covered: 22,762,917 out of 1,412,464,843

Uncovered: 23,610,954 out of 42,417,757
Matches: 13,511,992 out of 42,417,757
Mismatches: 5,288,726 out of 42,417,757
Insertions: 6,085 out of 42,417,757

Xenopus tropicalis

Uncovered: 1,496,215,028 out of 1,511,717,716
Covered: 15,502,688 out of 1,511,717,716

Uncovered: 17,929,847 out of 30,481,746
Matches: 9,009,773 out of 30,481,746
Mismatches: 3,537,551 out of 30,481,746
Insertions: 4,575 out of 30,481,746