Fig. 3: Characterization of alleles and stutters.

A Log₁₀ (P_r) plot for characterizing alleles and stutters of STR in all the merged reads obtained from TAS data of 16 human cell lines. Relative NRU at a STR locus were referred as increased or decreased NRU in sequencing reads in comparison to NRU of the STR sequence with the highest read count. The orange and black dots represented alleles and stutters, respectively. B P_r thresholds for different alleles. Compared to STR alleles with the highest read counts, the threshold for 2^nd adjacent alleles was P_r > 0.3, and for 2^nd nonadjacent alleles P_r > 0.1. C Three types of stutters at the STR loci: backward stutters, forward stutters and combined stutters. D S_r thresholds for different stutters. The threshold for n_a-1 and n_a + 1 adjacent stutters was S_r ≤ 0.12; and for n_a-2 and n_a + 2 nonadjacent stutters (and beyond) was S_r ≤ 0.01. E The threshold for combined stutters (between two alleles) was S_r ≤ 0.3 compared to the maximum read count. F, G S_r values of the individual STR loci of STRaM were calculated from (F, n = 3 independent experiments) T47D cells and (G, n = 16) 16 cell lines. The dash line indicated the S_r thresholds for stutters. H A summary of the P_r thresholds for alleles and S_r for stutters in the STRaM. Data were analyzed by student’s t test. Error bar, mean ± SEM.