Table 2 Summary of SSM/WGS data
Filtering Analysis (FA1–4)StrainNumber of Variants Before SSMNumber of Variants After SSM
Suppressed DNA ReadsNonsuppressed ReadsTotalChange in CodingaChange in Coding Manually Filtereda,b
TotalChange in CodingaTotal
FA1 100%Sup >0%Non-SupWY12082018210424,6563144
WY12092075222471,8574242
WY121020962301,021,9543732
WY12111898218860,4171922
WY12172063208969,2923600
FA2 ≥90%Sup >0%Non-SupWY12082652 (+31.4%)245424,65642 (+35.5%)44
WY12092845 (+37.1%)260471,85745 (+7.1%)42
WY12102732 (+30.3%)2581,021,95446 (+24.3%)65
WY12112347 (+23.7%)237860,41729 (+52.6%)55
WY12172734 (+32.5.%)239969,29241 (+13.9%)11
FA3 100%Sup ≥10%Non-SupWY1208201821097,520 (−77.0%)38 (+22.6%)55
WY12092075222117,834 (−75.0%)44 (+4.8%)53
WY1210189823074,586 (−92.6%)44 (+18.9%)32
WY1211206321891,174 (−89.4%)20 (+5.3%)22
WY1217189120879,897 (−91.8%)37 (+2.8%)00
FA4 ≥90%Sup ≥10%Non-SupWY1208265224597,52052 (+64.5%)55
WY12092845260117,83447 (+21.6%)53
WY1210273225874,58656 (+40.5%)65
WY1211234723791,17430 (+59.3%)55
WY1217273423979,89743 (+30.1%)11
  • Sequencing was carried out on pooled independent isolates from suppressed and nonsuppressed strains as described in Materials and Methods. Numbers in parentheses in indicate positive (+) or negative (−) percentage changes for each strain relative to FA1. For more information see Supplemental Methods, File S1.

  • a Includes nonsense, missense, frameshift, and splice site mutations.

  • b For specific details on manual filtering see File S1.