A SLIDER window is a small frame of DNA nucleotide positions that is defined by a begin position and an end position. There are four different ways in which a "window" can be defined in SLIDER: by "number of base pairs", by "number of polymorphic sites", by "dynamic sizing", and by "total surveyed length".
- Number of base pairs: Each window contains the same number of base pair positions lying within the segments of the surveyed region. The begin position of the first window is the start position of the first segment in the surveyed region. The window advances by adding a fixed window increment to the begin position of the previous window. This sum becomes the begin position of the next window, unless the position falls between two segments of the surveyed region, in which case the the begin position is set to the start position of the next segment, or the position falls beyond the stop position of the last segment, in which case the window advancement stops. The end position of each window is found by adding one less than the fixed window size to the window's begin position. If this position falls between two segments of the surveyed region, then the window will either span the gap between the two segments or jump to the next segment, depending on whether or not the gap percentage criterion is met.
- Number of segregating sites: Each window contains the same number of segregating sites. Because the number of segregating sites is fixed, the window size (in base pairs) is variable. The begin position of the first window is the start position of the first segment in the surveyed region. The end position of the first window is the position halfway between the nth and the (n + 1)st segregating sites, where n is the number of segregating sites in the window. The windows advance by 1 segregating site, so that the begin position of the next window is the position halfway between the positions of the first and second segegrating sites of the previous window, and the end position advances in a similar manner. If the begin position falls between two segments of the surveyed region, then the start position of the next segment becomes the new window begin position. If the end position falls between two segments, then ...
- Dynamic sizing: Each window is a complete segment of the surveyed region. The begin and end positions of a window correspond to the start and stop positions of a segment.
- Entire region: A single window contains all the segments of the surveyed region. The window's begin and end positions are the start position of the first segment and the stop position of the last segment, respectively.
When the sliding window is defined by the number of base pairs, the window size should be given in terms of the number of base pairs to be included in each window (the default value is 1000). The selected slider statistics will be calculated for each window of this length that falls within When the sliding window is defined by number of segregating sites, the sliding window size should be given in terms of the number of segregating sites that are to be included in each window (the default value is 5).
This value is used to increment the begin position of the sliding window. When the sliding window is defined by the number of base pairs, the window increment should be given in terms of the number of base pairs to advance the window (the default value is 100 bp). When the sliding window is defined by the number of segregating sites, the window increment is set to be 1 segregating site.
When the window is defined in terms of the number of base pairs, the window will span a gap between one or more surveyed segments only if the gap length is less than the gap percentage multiplied by the window size. When a gap is spanned by a window, the segments on either side of the gap are treated as if they were contiguous. For example, consider a surveyed region that is covered by two segments with site positions 1-1000 and 1200-2400, and thus has an intervening gap length of 199 base pairs. With the default settings (window size = 1000 bp, window increment = 100 bp, gap percentage = 50%), SLIDER's first window would begin at position 1 and end at position 1000. Because the window increment is 100 bp, SLIDER's window would advance to begin at position 101; however, it could not end at position 1101, since this position falls in the gap between the two segments. Instead, since 199 < 50% × 1000 and the gap percentage criterion is met, the second window would span the gap to end at position 1299 (the window includes the 1000 base pair positions 101-1000 and 1200-1299). On the other hand, if the gap percentage were set to say 10%, the gap percentage criterion would not be met, and the second window would instead jump to the start position of the second segment, and thus begin at position 1200 and end at position 2199. A window will span multiple gaps, if the gap percentage criterion is met for the sum of the gap lengths.
If 'True' is selected, haplotypes containing missing alleles are assumed to be completely unknown and are not included in the haplotype counts. If 'False' is selected, a haplotype with one or more missing alleles will be counted as the most commonly occurring known haplotype to which it could match.
Unless these are unchecked, the program assumes the symbols '?', 'N', 'n', and '-' (dash) represent missing alleles. You also have the option of entering your own string of characters to represent missing data.
If same letter is used in upper and lowercase to denote different alleles (e.g., 'A' and 'a'), select 'Yes'. Otherwise, the program will be case insensitive.
This is the minor allele (or derived allele, if ancestral data is present) threshold frequency that must be met in order for the polymorphic site to be included in the analysis.
If 'Yes' is selected, SLIDER will use the leading alphabetic characters of the individual ID's to determine the different sample populations within the data. For example, the individual names CA23, AA100, and CAU54 will create populations CA, AA, and CAU, respectively. SLIDER results will then be returned for each subpopulation, as well as for the total population.
The user can use this space to place information describing the SLIDER job. The job description will be written in the body of the email containing the SLIDER results. Any text is acceptable.
S is the number of polymorphic sites that are contained within the window. Under SLIDER's default settings, S is the number of biallelic sites.
Given that there are typically a different number of unknown alleles for each site within a window, SLIDER separately calculates the nucleotide diversity (πj) for each site using only those chromosomes for which the allele is known. For a single polymorphic site with K different alleles and missing data, the nucleotide diversity is
where xji is the number of chromosomes having allele ai at site j. If there are n chromosomes in the sample and m of these have missing data, then ∑xi = n - m. If the site is biallelic and has no missing data, the above formula for πj reduces to
Under an infinite sites model and the assumption of random mating, E(π) = θ and
With n chromosomes in the sample and S segregating sites in the window, θW is given by
where
Using the above definitions of Π and θW, Tajima's D is given by
