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What is the difference between Single Nucleotide Polymorphism (SNP), Mutation and Structural Variation(SV)?

Lets state what a Mutation is first. Mutation: A mutation is any change in an organism's genetic sequence which varies from that of the wild-type reference sequence (hg19/GrCH37 from 2009 or hg38/...
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Ancestral Allele explanation

SNP Let's start with the definition that has nothing to do with the rest of the question :). A Single-Nucleotide-Polymorphism (SNP) is a kind of genetic variation that you find in population. This ...
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Whole Genome Sequencing vs Whole Exome Sequencing

WES, almost certainly. First of all, the vast majority of phenotype-causing variants are found in exons. For most analyses that are looking into disease causing mutations, WGS is pointless. It only ...
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SNPs in the Human Genome

I was wondering how many SNPs there are in a single person on average A SNP is a polymorphism in the population, it is not a thing a haplotype can carry. Each individual has a given variant for any ...
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Trying to understand the big picture behind DNA sequencing, alignment and searching

Here's a quick summary of a few mis-hits in your otherwise good analysis: Not many bioinformatics applications use Hadoop, Apache Spark or Apache Flink. In fact, I have never heard of the Apache ...
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Statistician confused about exact SNP data type

SNP is not a specific data type but rather a biological phenomenon. The abbreviation "Single Nucleotide Polymorphism" only means there is a variability (between individuals) in a single ...
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Why perform imputation?

In GWAS we are interested in understanding which SNP has a causal influence on a specific phenotype. At the moment large scale studies are carried out by genotyping arrays. For each SNP we put on the ...
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Trying to understand the big picture behind DNA sequencing, alignment and searching

RAM's answer is very good, I'll just add on the computational side, short reads are error prone. That's important to account for when aligning or assembling. The reads themselves can just be ...
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What is the difference between a fixed substitution and a single nucleotide polymorphism (SNP)?

If you look into a certain population, you will find mutations (for example SNPs) in some ratio with the wild-type allele. When a mutation reaches fixation, it will be the only allele, reaching 100% ...
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Location of TFBS in genome

I would link your data with the ENCODE dataset. This dataset provides locations of TFBS. It is also accessible via the UCSC genome browser. For the actual question TFBS are located pretty much ...
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Genetic entropy

I'm new to this idea but did a bit of searching. The origin of this idea of "genetic entropy" appears to be a guy named John Sanford. He is also the author of the "waiting time problem" you reference....
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Personal Genomic Data Samples

Here is the link to the 1000 Genomes project, all the data is available for download. They already have a comprehensive list of SNPs as well. It is not the only project around but it is definitely the ...
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DNA Analysis (AncestryDNA)

These tests don't actually tell your ancestry, there is no way for a genetic test to do that because there is too much genetic variation among populations, as well as between. Instead, the test is ...
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Studying the epigenetic variability, can I use SNPs?

Starting from what appears to be your main question: Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed in the brain region? I would ...
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What's the role of SNP (Single Nucleotide Polymorphism) in a disease when there is no gene associated to that SNP

SNPs do not signify anything about the functionality of a particular piece of DNA. You can think of a SNP as just a sign that says "hey, something in my neighborhood might be interesting!!" ...
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Regarding the NCBI FTP site

Getting SNP data from FTP Site of NCBI SNP: It's actually simple to download the data from the NCBI, if you follow the method given by FAQ( as given by @WYSIWYG). Step 1: Goto organism FTP: ftp://...
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SNPs in DNase hypersensitive and histone marks sites

First off let's define some concepts. DNAse hypersensitive regions are DNA regions which are in an open chromatin conformation (i.e. euchromatin). This means that those regions are more active at the ...
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What fraction of sites are expected to be polymorphic?

Reiterating the above comments. Have a look at Tajima's D. It provides an estimate for the number of segregation sites for a population under a neutral mutation model. The general form of the ...
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What fraction of sites are expected to be polymorphic?

The fraction of polymorphic sites that exist in a population is dependent on the biology of the organism. For instance, you would expect to find different rates of polymorphism in related plants that ...
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Database of medically validated SNPs

You can search by traits (mostly diseases) for genome wide association, in these databases: Gwasdb2 Human genome variation Database: it also links to a Copy number Variation (CNV) database.
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Why do almost all SNPs have two alleles?

Well, though it is possible to have SNPs of more than two alleles, and some exist, due to the low probability of having a basepair change twice in the same base-pair (there are aproximately 3.000 Mb ...
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Parameters of Variant calling analysis

We will be needing some additional information to answer your question more completely: What sequencing platform are you using? Illumina HiSeq/MySeq; ...
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Analysis over single chromosome data

You can analyse a single chromosome. All the bioinformatics tools I know, allow that. Consider only the reads that map to the desired chromosome (or any segment of the genome). However, most next-gen ...
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Single copy housekeeping genes

Just flying from the waist: filter approach: If there is a data source that has the expression data for cells in multiple tissues for any organism i would use that to find the housekeeping genes by ...
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Single copy housekeeping genes

The following is probably a good set, it's for Arabidopsis you need to check if it fits with your need. CBP20 Gene Gene Locus: At5g44200 Actin-2 Gene Gene Locus: At3g18780 UBC Gene Gene Locus: ...
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Single copy housekeeping genes

There is no single answer for a gene. The most correct thing to do is to use a set of genes across many locus and measure the correlation of copy number across them first, and only use the ones which ...
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GEN file format, SNPs and alleles

From what I could find the .gen file format for SNPs was developed for the IMPUTE2 program and is generally meant to be a flexible file format for SNP data. The ...
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Which side of the DNA helix is used for describing SNPs?

It is described with respect to the reference sequence. See the VCF format description.
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Which side of the DNA helix is used for describing SNPs?

DNA has a "sense" strand and an antisense strand. The sense strand for that gene is the one you care about when discussing SNPs in that gene, because its the one being transcribed (and, as a result, ...
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