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Zebrafish vs Medaka Translated Blat alignments

Zebrafish (Danio rerio, Zv9) 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 60. 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 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} {default_soft_masking => 1}

Results

Number of alignment blocks: 365,231

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

Uncovered: 1,373,495,115 out of 1,412,464,843
Covered: 38,969,728 out of 1,412,464,843

Uncovered: 17,258,806 out of 42,417,757
Matches: 18,852,937 out of 42,417,757
Mismatches: 6,293,924 out of 42,417,757
Insertions: 12,090 out of 42,417,757

Oryzias latipes

Uncovered: 841,545,855 out of 868,983,502
Covered: 27,437,647 out of 868,983,502

Uncovered: 12,377,731 out of 30,193,605
Matches: 13,428,433 out of 30,193,605
Mismatches: 4,374,881 out of 30,193,605
Insertions: 12,560 out of 30,193,605