Recently, crAssphage has been proposed as a human-specific marker for tracking 
fecal contamination. However, its performance has always been validated in a 
limited number of host samples, which may obscure our understanding of its 
utility. Furthermore, few studies have quantified confidence of fecal 
contamination when using crAssphage. Here, we evaluate the performance and 
confidence of crAssphage by analyzing a large panel of metagenomic data sets 
combined with Bayesian analyses. Results demonstrate that crAssphage exhibits 
superior performance with high host sensitivity and specificity, indicating its 
suitability for tracking human fecal sources. With the marker, a high confidence 
(>90%) can be obtained and particularly, multiple samples with positive results 
provide a near certainty of confidence. The application of crAssphage in the 
sediments of three Chinese urban rivers shows a high confidence of >97% of human 
fecal contamination, suggesting the serious challenge of sewage pollution in 
these environments. Additionally, significant correlation is observed between 
crAssphage and antibiotic resistance genes (ARGs), expanding the utilization of 
crAssphage for pollution management of ARGs. This study highlights the benefit 
of using metagenomic-based analysis for evaluating the performance and 
confidence of microbial source tracking markers in the coming era of big data 
with increasing resources in available metagenomic data.