Fig. 6

diffBUM-HMM detects more differentially reactive nucleotides (DRNs) in the Xist lncRNA that are preferentially single-stranded A’s and U’s. A diffBUM-HMM calls more single nucleotide stretches as DRNs. The barplots show the distribution of the length of stretches of nucleotides that were called DRNs by diffBUM-HMM and deltaSHAPE in the in vivo data and ex vivo data. B The comparison between all the DRNs called by diffBUM-HMM, including the data normalized to the denatured data, those uniquely detected by diffBUM-HMM, and the results from the deltaSHAPE analyses on the two replicates individually. diffBUM-HMM DRNs are mostly A’s and U’s and enriched in regions predicted to be single-stranded in Xist. DRNs identified by diffBUM-HMM are preferentially located in Xist single-stranded regions. “Den norm” indicates the data where we normalized the mutation frequencies of treated and control samples based on the denatured RNA data. “diffBUM-HMM (unique)” indicates those DRNs that were uniquely detected by diffBUM-HMM