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Zebrafish vs Lamprey Translated Blat alignments

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

Zebrafish Lamprey
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: 98,200

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

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

Petromyzon marinus

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