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Human vs Lamprey Translated Blat alignments

Human (Homo sapiens, GRCh37) 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 63. Human 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

Human Lamprey
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}

Results

Number of alignment blocks: 95,999

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 3,088,002,537 out of 3,098,825,702
Covered: 10,823,165 out of 3,098,825,702

Uncovered: 27,154,720 out of 35,313,516
Matches: 5,844,951 out of 35,313,516
Mismatches: 2,312,505 out of 35,313,516
Insertions: 1,340 out of 35,313,516

Petromyzon marinus

Uncovered: 879,481,421 out of 885,534,757
Covered: 6,053,336 out of 885,534,757

Uncovered: 7,721,745 out of 12,529,983
Matches: 3,412,589 out of 12,529,983
Mismatches: 1,394,554 out of 12,529,983
Insertions: 1,095 out of 12,529,983