Transition to Transversion Ratio

The transition to transversion ratio (Ti/Tv) compares the number of transition mutations to the number of transversion mutations observed within a sequence. Due to there being twice as many possible transversions to transitions, we would expect a Ti/Tv of 0.5. However, this changes when we take into consideration biological context. In human genomes, this expected Ti/Tv can range anywhere from ~2.0 to ~3.3. The ratio is also highly depenedant on genomic region, ancestry, analysis pipelines, filtering etc. As a QC, it can be used to evaluate the quality of a sequence of SNPs for technical errors. A Ti/Tv closer to the theroretical 0.5 value can indicate sequencing errors (as these errors mimic random mutation rates) and extremely high Ti/Tv values (>4) can indicate high bias in analysis. [@gatk2024qc; @cdgenomics2026; @wang2015; @carson2014]

Mutational Spectrum Plot

Here, we break down all mutations in a sample according to each type of mutation. There are six possible mutations. [@griffithlab2017]

References:

Broad Institute GATK Documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360035531572-Evaluating-the-quality-of-a-germline-short-variant-callset

CD Genomics Technical Resource: https://www.cd-genomics.com/resource-quality-control-whole-exome-sequencing.html

PMID: 25297068, 24884706

Principal Component Analysis (PCA)

PCA is a statistical method used to simplify high-dimensional genetic data (such as millions of SNPs) into a small number of continuous axes called principal components (PCs). This is useful to infer ancestry and investigate population structure. It can also be used to check for batch effects in your dataset. [@wickland2021]

References:

PMID: 33861770

Adding a note regarding the interactivity of the figures:

"Note: All visualizations are interactive and can be manipulated to obtain additional information."

The Allele Balance is the ratio of sequence reads supporting a specific allele compared to the total number of reads covering that genomic position, i.e. it measures the proportion of sequencing reads supporting a specific allele relative to the total reads at a given locus for a single sample. Ideally, you want the AB ratio of your heterozygous loci (0/1) to be ~0.5 (ideal: 50% ref, 50% alt reads) and the homozygous loci (reference 0/0 and alternate 1/1) ~0.0 (Ideal: 0% alt reads) and ~1.0 (Ideal: 100% alt reads) respectively. However, what we see in practice is that true variants cluster around these discrete theoretical ratios. In filtering pipelines, calls deviating significantly from the theoretical thresholds are typically filtered out as false positives caused by strand bias, PCR duplication, or misaligned reads.

The second quality evaluated in this filter is GQ and AD. The specifics of these parameters are detailed in section 1.1. You will se that we plot the AB vs GQ and AD.

Variants that fail to pass all three metrics will be removed.

QC has now been done. In this section, we will now filter the variants based on functional and quality information. These filters are designed to enrich for rare variants with a predicted functional impact, i.e. a variant that has some evidence for pathogenicity and biological relevance.

в каком смысле дополняет? как слагаемое при сумме? или добавляет детали?

{Quality Assurance}

{Services}

{Community Advice}

{Data Typing} {Multiple Resolution}

“Ambition is good. Ambition is right. Ambition works.” Gordon Gekko in the movie Wall Street (actually on greed, but works this way too ;-))

Show us two actions he is done at same time "He clambers out, tugs on some clothes and, magician-like, pulls the coins "

1. Ironic that this reference is ostensibly about the usage of "first-class citizen" in society, yet it links to a seemingly-mismatched (by name only, that is) article, entitled "second-class citizen".

2. Ironic that the first-class (unqualified) article is about the figurative meaning of "citizen" used in computer science, and that the page describing first-class and second-class status of the more literal citizens in society is relegated to what I kind of think is a second-class position in the encyclopedia (because it takes the #2 position numerically, even though it is (at least as is implied in this reference) also about first-class citizens (though the word "first-class" does not appear a single time in that article, so maybe this reference is the one that is more ironic/incorrect).

rare to see "internet" used to mean an internetwork in the general sense

Python-igraph 0.8.3. (2020, October 8). Igraph Support Forum. https://igraph.discourse.group/t/python-igraph-0-8-3/473

Understanding the great-than-additive effect of these signaling molecules working in concert is important. Some students in the summer 2020 class were unsure what this meant, so it may be helpful to add to this description to clarify this greater-than-additive effect, which can also be described as synergistic. This could be something like, "The simultaneous signaling of all three of these molecules produces a synergistic effect that is stronger than the sum of the effects they each produce separately."

Being a teenager is hard; there are constant social and emotional pressures that have just been introduced into the life of a middle or high schooler, which combines with puberty to create a ticking time bomb. By looking at the constant exposure to unreasonable expectations smartphones and social media create, we can see that smartphones are leading to an increased level of depression and anxiety in teenagers, an important issue because we need to find a safe way to use smartphones for the furture generations that are growing up with them. Social media is a large part of a majority of young adults life, whether it includes Instagram, Facebook, Snapchat, Twitter, or some combination of these platforms, most kids have some sort of presence online. Sites like Facebook and Instagram provide friends with a snapshot of an event that happened in your life, and people tend to share the positive events online, but this creates a dangerous impact on the person scrolling.​ When teens spend hours scrolling through excluisvely happy posts, it creates an unrealistic expectation for how real life should be. Without context, teenagers often feel as if their own life is not measuring up to all of their happy friends, but real-life will never measure up to the perfect ones expressed online. Picture Picture Furthermore, social media sites create a way for teenagers to seek external validation from likes and comments, but when the reactions online are not perceived as enough it dramatically alters a young adults self-confidence. This leads to the issue of cyberbullying. There are no restrictions on what you can say online, sometimes even annonimously, so often people choose to send negative messages online. Bullying is not a new concept, but with online bullying, there is little to no escape as a smartphone can be with a teenager everywhere, and wherever the smartphone goes the bullying follows.This makes cyberbullying a very effective way to decrease a youth's mental health, in fact, cyberbullying triples the risk of suicide in adolescents, which is already the third leading cause of death for this age group.

The music we listen to highly impacts our decision making, especially as adolescents. Adolescents are extremely impressionable, and the music they listen to has a great impact on how they decide to live their day to day lives. Popular musicians are seen as role models by the people who idolize them, and adolescents may try to represents the songs in which they favor through their actions every day.

Recent studies have found that adolescents who listen to music that supports substance abuse and violence have a greater chance to act upon what they listen to. What young adults and teenagers listen to through music and popular media will affect their decision making process. Specifically with substance abuse, and there is a direct uptake in use of illegal substances by adolescents who listen to music that promotes such activities. This can cause a whole societal problem considering most of todays popular music among adolescents touches upon substance abuse and violence. Adolescents are extremely impressionable and the music they listen can shape how a person tries to act, or represent themselves.

Perhaps this is worth a reason number 4, or addition to number 3: Colleagues are warned about a problem they might encounter themselves in the future, and will know to come to you when facing a similar issue.

We mention Firebug here. Should we also refer readers to Firefox Developer Tools?