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Human vs Chicken Translated Blat alignments

Human (Homo sapiens, GRCh37) and Chicken (Gallus gallus, Galgal4) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 71. 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 Chicken
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: 350,665

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

Uncovered: 3,058,352,463 out of 3,098,825,702
Covered: 40,473,239 out of 3,098,825,702

Uncovered: 14,818,456 out of 35,270,662
Matches: 15,937,830 out of 35,270,662
Mismatches: 4,503,616 out of 35,270,662
Insertions: 10,760 out of 35,270,662

Gallus gallus

Uncovered: 1,014,108,365 out of 1,046,932,099
Covered: 32,823,734 out of 1,046,932,099

Uncovered: 8,119,244 out of 25,934,237
Matches: 13,961,332 out of 25,934,237
Mismatches: 3,844,763 out of 25,934,237
Insertions: 8,898 out of 25,934,237