GC bias describes the relationship between GC content and read coverage across a genome. That is, a genomic region of a higher GC content tends to have more (or less) Illumina reads covering that region.
GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data.
GC content correlates tightly with coverage biases. The PacBio and HiSeq platforms also evidenced similar profiles of GC.
- GC bias一般指测序过程中，序列本身的GC含量给测序以及组装带来的偏差
- 在 PCR 过程中，遇到 G、C 碱基时，PCR 的效率会降低，由此导致的当 G、C 含量偏高的序列时产生的 reads 数偏少，这种现象称为「GC Bias」
- GC skew也即GC歪斜或GC偏倚，用来衡量在单链DNA中碱基G和C相对含量的不同。双链DNA其G的含量一定等于C的含量，然而G和C在每条单链的含量不一定相同，在每条单链中G与C含量的偏移就叫GC skew。其具体的计算方法为(nG–nC)/(nG+nC)，因此GC skew+就表示G的含量大于C，GC skew-表示G的含量小于C
GC skew is a parameter that represents the amount bias of G and C in a single DNA molecule strand and its formula is (C-G)/(C+G).
Chargaff's salt distribution law's second term defines that the quantity of G and C becomes almost the same, this phenomena occurs in the hole genome, but bias can be seen in small set regions. In fact in some bacteria this tendency can be seen to be shifting elegantly in different places, moreover it is known that those places match replication origin/terminus. There are two theories about how GC skew phenomena occurs, these are different mutation probability in leading strand and lagging strand and mutation bias by usage of codons.
在大多数细菌基因组中，DNA复制中的前导链（leading strand）和对应的滞后链（lagging strand）在碱基组成上存在着很明显的不同，表现出碱基组成上的不对称性（compositional asymmetry）。前导链富含G和T，而滞后链中的A和C更多一些，打破A=T和C=G的碱基概率期望而发生偏移，而且通常GC偏移比AT偏移发生的更明显，所以习惯上更多地只考虑GC偏移。因此从复制起点延伸的前导链中是GC skew+，而在滞后链中为GC skew-，所以GC skew值是前导链起点、终点以及转变成滞后链的信号，这使得GC skew分析成为在环状DNA中标记复制起点的一个有用工具。
[参考链接]（https://www.jianshu.com/p/9e30cec7f208）
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