. 2021 Mar 3;12:1424. doi: 10.1038/s41467-021-21592-8

Table 1.

Summary of notation and terminology used in the paper.

Notation	Description	Synonym in text	Observable
i	Individual index.	—	—
h	Haplotype index, with h = 1, 2 for diploid.	—	—
$X_{i}^{h}$	Alternative allele count (0 or 1) of the variant linking to the gene haplotype h.	Allelic dosage	Yes
L_i	The total number of reads in the RNA-seq library.	Library size	Yes
$Y_{i}^{h}$	Count of reads originated from gene haplotype h.	Haplotypic (read) count	No
$Y_{i}^{(h) obs}$	Allele-specific read count that gets aligned to the gene haplotype h.	Allele-specific (read) count	Yes
$Y_{i}^{total}$	Total count of reads originated from any of the two gene haplotypes (sum).	Total (read) count	Yes
θ_0,i	The abundance of the gene haplotype relative to the total transcriptome when the linked causal variants are all in reference alleles	Baseline (relative) abundance	No
$θ_{i}^{h}$	The abundance of the gene haplotype h relative to the total transcriptome in individual i	(Relative) abundance; expression level^a	No
β	The log fold change of gene haplotype abundance when linking to alternative allele relative the reference allele	Allelic fold change (aFC) in natural log scale	No
$\frac{Y_{i}^{(1) obs}}{Y_{i}^{(2) obs}}$	The ratio of the allele-specific counts between two haplotypes	Allelic imbalance	Yes
$Y_{i}^{trc}$	Shorthand of the term $\log \frac{Y_{i}^{total}}{2 L_{i}}$ .	—	—
$Y_{i}^{asc}$	Shorthand of the term $\log \frac{Y_{i}^{(1) obs}}{Y_{i}^{(2) obs}}$	—	—
θ	Only used in simulation where θ = E(θ_0,i)	expression level^b	—

The "Description” column contains a brief definition of each "Notation”, and the "Synonym in text” column contains the corresponding terminology used in the text. The "Observable” column indicates whether the entity is an observable variable or not.

^a,bExpression level does not strictly refer to $θ_{i}^{h}$ or E(θ_0,i), but, more generally, it refers to the abundance of the gene transcripts relative to the transcriptome.