VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples

BMC Bioinformatics

Table 1 Comparison of true and estimated variant proportions for the synthetic mixtures

Mixture name		B.1.1.7	B.1.160	B.1.177	B.1.258	Other
Ont-long-1	True	0.19	0.42	0.23	0.16	0.00
	VirPool	0.18	0.42	0.23	0.17	0.00
	Median	0.19	0.43	0.24	0.17	− 0.03
Ont-long-2	True	0.17	0.38	0.21	0.15	0.09
	VirPool	0.16	0.38	0.22	0.15	0.09
	Median	0.17	0.38	0.20	0.15	0.09
Ont-long-3	True	0.42	0.00	0.00	0.35	0.23
	VirPool	0.41	0.00	0.00	0.37	0.22
	Median	0.39	0.01	0.02	0.36	0.23
Ont-long-4	True	0.00	0.65	0.35	0.00	0.00
	VirPool	0.00	0.64	0.36	0.00	0.00
	Median	0.01	0.63	0.43	0.02	− 0.08
Ont-short-1	True	0.19	0.42	0.23	0.16	0.00
	VirPool	0.18	0.42	0.23	0.17	0.00
	Median	0.19	0.43	0.24	0.17	− 0.03
Ont-short-2	True	0.17	0.38	0.21	0.15	0.09
	VirPool	0.16	0.38	0.22	0.15	0.09
	Median	0.17	0.38	0.20	0.15	0.09
Ont-short-3	True	0.42	0.00	0.00	0.35	0.23
	VirPool	0.41	0.00	0.00	0.37	0.22
	Median	0.39	0.01	0.02	0.36	0.23
Ont-short-4	True	0.00	0.65	0.35	0.00	0.00
	VirPool	0.00	0.64	0.36	0.00	0.00
	Median	0.01	0.63	0.43	0.02	-0.08
Illumina-1	True	0.15	0.23	0.27	0.34	0.00
	VirPool	0.16	0.26	0.29	0.29	0.00
	Median	0.20	0.26	0.30	0.35	− 0.11
Illumina-2	True	0.13	0.20	0.23	0.29	0.16
	VirPool	0.14	0.22	0.25	0.25	0.13
	Median	0.17	0.23	0.25	0.30	0.06
Illumina-3	True	0.16	0.25	0.00	0.37	0.21
	VirPool	0.18	0.29	0.01	0.33	0.19
	Median	0.23	0.32	0.00	0.38	0.07
Illumina-4	True	0.00	0.46	0.54	0.00	0.00
	VirPool	0.00	0.47	0.53	0.00	0.00
	Median	0.00	0.49	0.66	0.00	− 0.16

The first group corresponds to mixtures created with Oxford Nanopore reads with long (2 kbp) amplicons, the second group corresponds to mixtures created with Oxford Nanopore reads with short (400 bp) amplicons, and the third group corresponds to mixtures created with Illumina reads. The proportion of other for the median estimator is calculated as 1 minus the sum of the estimated proportions (therefore it can be negative)

ISSN: 1471-2105