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Zebrafish vs Lamprey Translated Blat Results

Zebrafish (Danio rerio, Zv9) and Lamprey (Petromyzon marinus, Pmarinus_7.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 64. 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

ParameterZebrafishLamprey
Chunk size1,000,00025,000
Overlap10,00010,000
Group set size100,000,00010,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 98,200 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Zebrafish

Uncovered: 1,401,102,989 out of 1,412,464,843
Covered: 11,361,854 out of 1,412,464,843

Uncovered: 32,281,096 out of 42,417,757
Matches: 7,260,425 out of 42,417,757
Mismatches: 2,874,923 out of 42,417,757
Insertions: 1,313 out of 42,417,757

Lamprey

Uncovered: 879,368,912 out of 885,534,757
Covered: 6,165,845 out of 885,534,757

Uncovered: 7,644,781 out of 12,529,983
Matches: 3,473,826 out of 12,529,983
Mismatches: 1,410,274 out of 12,529,983
Insertions: 1,102 out of 12,529,983