Additional file 2 of Genome-wide association reveals host-specific genomic traits in Escherichia coli
dataset
posted on 2023-04-13, 14:03 authored by Sumeet K. Tiwari, Boas C. L. van der Putten, Thilo M. Fuchs, Trung N. Vinh, Martin Bootsma, Rik Oldenkamp, Roberto La Ragione, Sebastien Matamoros, Ngo T. Hoa, Christian Berens, Joy Leng, Julio Álvarez, Marta Ferrandis-Vila, Jenny M. Ritchie, Angelika Fruth, Stefan Schwarz, Lucas Domínguez, María Ugarte-Ruiz, Astrid Bethe, Charlotte Huber, Vanessa Johanns, Ivonne Stamm, Lothar H. Wieler, Christa Ewers, Amanda Fivian-Hughes, Herbert Schmidt, Christian Menge, Torsten Semmler, Constance SchultszAdditional file 2: Table S1. Metadata of 1,198 E. coli isolates. Table S2. Genes and genetic variants associated with different hosts that came as significant by both k-mer based as well as pan-genome based GWAS. Table S3. Prevalence of ompP, arlC and ompT in different STs in the RefSeq collection (n=17,994) and in our collection of E. coli isolates (n=1198). Table S4. Prevalence of the iroBCDEN gene cluster in sequence types and associated hosts. Details are shown for sequence types (STs) with at least ten isolates harboring iroBCDEN. Table S5. Genomes from our dataset used for annotating host-associated k-mers.
