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Human vs Platyfish Translated Blat alignments

Human (Homo sapiens, GRCh37) and Platyfish (Xiphophorus maculatus, Xipmac4.4.2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 69. 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 Platyfish
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: 189,865

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

Uncovered: 3,078,269,352 out of 3,098,825,702
Covered: 20,556,350 out of 3,098,825,702

Uncovered: 20,303,530 out of 35,313,516
Matches: 10,930,350 out of 35,313,516
Mismatches: 4,074,741 out of 35,313,516
Insertions: 4,895 out of 35,313,516

Xiphophorus maculatus

Uncovered: 714,234,768 out of 729,662,853
Covered: 15,428,085 out of 729,662,853

Uncovered: 20,316,816 out of 33,480,785
Matches: 9,587,963 out of 33,480,785
Mismatches: 3,570,159 out of 33,480,785
Insertions: 5,847 out of 33,480,785