My teacher explained it using Mendelian laws of inheritance, stating that unrelated alleles that followed Mendelian Inheritance will be in equilibrium. I.e. they wouldn't be linked. However, disequilibrium (Positive or negative) demonstrates linking. I think it is a similar point of view, and this girl really got it!! Not many people speak up in class like that kudos to her.

I don’t know if this is what she meant as well but the way I explain it to myself is that it means the linkages between all possible variants are equal, indicated through likelihood of coinheritance. But when variants are more like to be inherited together than others, the links between those variants are stronger, implying the inheritance between all possible variants are not equal

Yes, as you described clearly, they are different concepts. The hypothesis of correlation between TAD spans and LD blocks was raised since a plausible interaction between recombination machinery and chromatin condensation could drive such patterns. However, this was not detected: www.ncbi.nlm.nih.gov/pmc/articles/PMC6396425/ . On the other hand, conservation between individuals and across regions of the genome might suggest that certain haplotypes may be enriched (as a result of selection): "One consequence is that entire TADs or sub-TADs do not typically segregate as single haplotypes in human populations, enabling independent selection on regulatory variants versus the promoter and coding variants of their target genes. Furthermore, large LD blocks that span chromatin domain boundaries indicate that regulatory and coding variants from one domain can segregate with variants from the adjacent domain. The fact that haplotype breakpoints do not align with chromatin boundaries may indicate that recombination is deleterious at these functional elements. These findings are different from observations regarding fixed structural differences between genomes of various mammals, which tend to preserve TADs with breakpoints enriched at TAD boundaries (Krefting et al. 2018; Lazar et al. 2018). We therefore conclude that, while chromatin domains are functional genomic entities maintained as syntenic units over evolutionary time, recombination is largely independent of interphase chromatin structure. This creates novel haplotypes of the genomic elements within TADs on which selection can operate."

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FASTQ (Raw Sequence Data) FASTQ is a text-based format for storing both nucleotide sequences and their corresponding quality scores. It is widely used in high-throughput sequencing. File Structure: Header Line: Starts with '@' followed by a sequence identifier. Sequence Line: Contains the nucleotide sequence. Plus Line: Starts with a '+' and may be followed by the same sequence identifier. Quality Line: Contains quality scores for each nucleotide in the sequence, encoded as ASCII characters

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Imagine a single strand of DNA that in it exist regions that are known to mutate. These smaller informative segments are called Markers. Their specific sequence can vary, so there are different versions of this sequence. These versions are called Alleles. Alleles can be different among themselves just in one position. Ex Allele A is: CTTTA Allele B is: CTTTC Allele A is: CTTTT A given Marker can have Allele A or B or C. This is true for all markers that we analyse on a given strand. It follows that a Haplotype is a set of Markers with a specific allele makeup in each one of them. As an example a Haplotype composed by three markers: Haplotype 1: Allele A in Marker 1; Allele Z in Marker 2; Allele H in Marker 3. Haplotype 2: Allele A in Marker 1; Allele Z in Marker 2; Allele I in Marker 3. Haplotype 3: Allele A in Marker 1; Allele X in Marker 2; Allele J in Marker 3. Simplifying: Haplotype 1 is composed by the set of Alleles A,Z,H Haplotype 2 maintains Allele A in the first region (marker) and Allele Z in the second region, but it differs in the third region of the strand; theres an I allele instead of the H of the first Haplotype. Haplotype 3, following the same approach, is composed instead by the alleles A, X and J in the same strand regions (markers) as the previous two haplotypes. An Haplogroup is when a group of people whose haplotypes have all or most of the same marker alleles in common.