Nucleotide Diversity

What is nucleotide diversity and why is it important?

1. High nucleotide diversity: when a library has roughly equal proportions of all 4 nucleotides in every cycle of the run
2. The diagram below illustrates the diversity and base-balance of well-balanced and unbalanced libraries, and how that can be reflected in the % base plot of Sequencing Analysis Viewer(SAV)

[fig 1] Illustrates of the diversity and base-balance

Why is nucleotide diversity important?

1. Nucleotide diversity is required for effective template generation and is important for the generation of high-quality data
2. Diversity is especially important during the first 4-7 cycles of the first sequencing read for MiniSeq, MiSeq, NextSeq, and HiSeq 1000-2500 systems. The Sequencing software uses images from these early cycles to identify the location of each cluster in a process called template generation
3. Diversity is also important for the first 25 cycles because this is when phasing/pre-phasing, color matrix corrections, and the pass filter calculations occur
4. Real-Time Analysis(RTA) software need a proper PhiX is spiked-in. You can find more specific data in here

ref)

https://support.illumina.com/bulletins/2016/07/what-is-nucleotide-diversity-and-why-is-it-important.html