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chain-format.scroll
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chain-format.scroll
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import ../code/conceptPage.scroll
id chain-format
name chain-format
appeared 2013
tags textDataFormat
conceptDescription The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. Each set of chain alignments starts with a header line, contains one or more alignment data lines, and terminates with a blank line. The format is deliberately quite dense.
fileType text
centralPackageRepositoryCount 0
country United States
originCommunity University of California, Santa Cruz
reference https://genome.ucsc.edu/goldenPath/help/chain.html
example
chain 4900 chrY 58368225 + 25985403 25985638 chr5 151006098 - 43257292 43257528 1
9 1 0
10 0 5
61 4 0
16 0 4
42 3 0
16 0 8
14 1 0
3 7 0
48
chain 4900 chrY 58368225 + 25985406 25985566 chr5 151006098 - 43549808 43549970 2
16 0 2
60 4 0
10 0 4
70