Manhattan Plot.

The first step in any statistical analysis should always be eyeballing the data. But how do you eyeball the data from the entire human genome all at once? The answer is the Manhattan Plot. It gains its name from the similarity of such a plot to the Manhattan skyline: a profile of skyscrapers towering above the lower level “buildings” which vary around a lower height.

Associations between regions on the whole genome and any factor such as disease resistance, gets a non-zero value.

Genome locations along the entire human genome are plotted on the x axis, each dot on the Manhattan plot signifies a SNP. Each chromosome is given a different colour, The strongest associations have the smallest P-values (e.g., 10^−15), so the negative logarithm of P is plotted on the Y axis. We eyeball the result to find the locations with the largest Y values.

The eyeballing is a huge help in distinguishing between real associations and statistical outliers from a random distribution.

https://www.youtube.com/watch?v=Pdic7p_dk0I

So how many points plotted there?

The Rev Dodgson said:

So how many points plotted there?

According to one web source, 10 million points.

“SNPs occur throughout the human genome—about one in every 300 nucleotide base pairs. This translates to about 10 million SNPs within the 3-billion-nucleotide human genome. … A single-nucleotide polymorphism is a substitution of a single nucleotide, present at a level of more than 1% in the population.”

What I want to know is what it would make of my genome? I have parts of chromosomes 3 and 12 transposed, so instead of my chromosome 3 having a uniform colour, it should share the colours of chromosome 3 and 12, and the same for chromosome 12. I bet they don’t get it right, though.

mollwollfumble said:

The Rev Dodgson said:

So how many points plotted there?

According to one web source, 10 million points.

“SNPs occur throughout the human genome—about one in every 300 nucleotide base pairs. This translates to about 10 million SNPs within the 3-billion-nucleotide human genome. … A single-nucleotide polymorphism is a substitution of a single nucleotide, present at a level of more than 1% in the population.”

What I want to know is what it would make of my genome? I have parts of chromosomes 3 and 12 transposed, so instead of my chromosome 3 having a uniform colour, it should share the colours of chromosome 3 and 12, and the same for chromosome 12.

No it shouldn’t.

poikilotherm said:

mollwollfumble said:

The Rev Dodgson said:

So how many points plotted there?

According to one web source, 10 million points.

“SNPs occur throughout the human genome—about one in every 300 nucleotide base pairs. This translates to about 10 million SNPs within the 3-billion-nucleotide human genome. … A single-nucleotide polymorphism is a substitution of a single nucleotide, present at a level of more than 1% in the population.”

What I want to know is what it would make of my genome? I have parts of chromosomes 3 and 12 transposed, so instead of my chromosome 3 having a uniform colour, it should share the colours of chromosome 3 and 12, and the same for chromosome 12.

No it shouldn’t.

OK. Whatever you say.