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Human vs Coelacanth Translated Blat alignments

Human (Homo sapiens, GRCh37) and Coelacanth (Latimeria chalumnae, LatCha1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 66. 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 Coelacanth
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}

Results

Number of alignment blocks: 251,730

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

Uncovered: 3,069,377,098 out of 3,098,825,702
Covered: 29,448,604 out of 3,098,825,702

Uncovered: 16,713,423 out of 35,313,516
Matches: 13,939,277 out of 35,313,516
Mismatches: 4,652,811 out of 35,313,516
Insertions: 8,005 out of 35,313,516

Latimeria chalumnae

Uncovered: 2,836,963,967 out of 2,860,591,921
Covered: 23,627,954 out of 2,860,591,921

Uncovered: 14,939,946 out of 30,870,617
Matches: 11,962,041 out of 30,870,617
Mismatches: 3,961,735 out of 30,870,617
Insertions: 6,895 out of 30,870,617