Table 1.

Samples with whole genome sequencing data in our cohort of repeats collected 11 days or more after the first positive.

Days after the first positive	Genomes with high quality			Genomes with low quality			p value
	Number	Average Ct	Stdev	Number	Average Ct	Stdev
11- 20	28	21.1	5.7	43	31.2	2.3	0.00006
21-50	25	21.1	5.7	46	30.4	6.5	0.02
51+	14	19.3	4.9	66	31.4	2.3	0.0009
total	67	20.24	5.4	155	31.24	4.2	1.00E-09

High quality genomes were defined as sequences with coverage >90% and a mean depth of >100. Ct, cycle threshold; stdev, standard deviation.