Additional iSNV quality control information.

Subplot a. shows variant frequencies generated using the Wisconsin bioinformatic pipelines are shown on the x-axis and frequencies generated using the Washington bioinformatic pipeline are shown on the y-axis. The yellow box highlights low-frequency variants (3–15%), which is expanded out to the right. b. Proportion of intersection iSNVs relative to the total number of iSNVs increases as variant frequency threshold increases. c. The total number of iSNVs detected across both Twist RNA control replicates compared to the iSNV frequency threshold. 57/102 of iSNVs detected in these clonal samples occur <3% frequency. Note that the iSNVs reported in S1 Table are intersection iSNVs only. The identities of all iSNVs detected ≥1% frequency in the Twist RNA control can be found in the GitHub accompanything this manuscript. d. The number of intersection variants, both consensus and iSNVs, is compared to the Ct value for all samples where a Ct value was available. Out of 133 total samples, Ct values were available for 94. e. The number of intersection variants, both consensus and iSNVs, is compared to the RLU (relative light unit) value for all samples where a RLU value was available.

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