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show-snps

By Salzberg S., Delcher A., Last update 1494698999
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show-snps description

Show-snps is a utility program for reporting polymorphisms contained in a delta encoded alignment file output by NUCmer or PROmer. It catalogs all of the single nucleotide polymorphisms (SNPs) and insertions or deletions within the delta file alignments. Polymorphisms are reported one per line, in a delimited fashion similar to show-coords. Output is slightly different depending on which command switches are set. For instance, by default the output is arranged in a table style, however if the -T option is active, the output will be tab-delimited. Also, the sequence files, alignment type and column headers are output by default, however if the -H option is active, the headers will be stripped from the output. Other options like -l -C -x will add or remove columns from the output. So, for description purposes, all possible column headers will be given and it is up to the user to pair the column header with the column number. The descriptions for each header tag follows. (P1) position of the SNP in the reference sequence. For indels, this position refers to the 1-based position of the first character before the indel, e.g. for an indel at the very beginning of a sequence this would report 0. For indels on the reverse strand, this position refers to the forward-strand position of the first character before indel on the reverse-strand, e.g. for an indel at the very end of a reverse complemented sequence this would report 1. (SUB) character or gap at this position in the reference (SUB) character or gap at this position in the query (P2) position of the SNP in the query sequence (BUFF) distance from this SNP to the nearest mismatch (end of alignment, indel, SNP, etc) in the same alignment (DIST) distance from this SNP to the nearest sequence end (R) number of repeat alignments which cover this reference position (Q) number of repeat alignments which cover this query position (LEN R) length of the reference sequence (LEN Q) length of the query sequence (CTX R) surrounding reference context (CTX Q) surrounding query context (FRM) sequence direction (NUCmer) or reading frame (PROmer) (TAGS) the reference and query FastA IDs respectively. All positions are relative to the forward strand of the DNA input sequence, while the (BUFF) distance is relative to the sorted sequence.


Parent program: MUMmer

MUMmer or 'Maximal Unique Matches' is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes to one another. In recent years it has become a popular algorithm for comparing genome assemblies to one another, which allows scientists to determine how a genome has changed after adding more DNA sequence or after running a different genome assembly program.