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Human vs Zebra Finch Translated Blat alignments

Human (Homo sapiens, GRCh37) and Zebra Finch (Taeniopygia guttata, taeGut3.2.4) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 55. 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 Zebra Finch
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: 343,747

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

Uncovered: 3,059,939,781 out of 3,098,825,702
Covered: 38,885,921 out of 3,098,825,702

Uncovered: 15,774,198 out of 35,313,516
Matches: 15,232,543 out of 35,313,516
Mismatches: 4,295,922 out of 35,313,516
Insertions: 10,853 out of 35,313,516

Taeniopygia guttata

Uncovered: 1,202,026,267 out of 1,233,169,488
Covered: 31,143,221 out of 1,233,169,488

Uncovered: 7,530,580 out of 23,643,636
Matches: 12,646,312 out of 23,643,636
Mismatches: 3,459,303 out of 23,643,636
Insertions: 7,441 out of 23,643,636