I have recently sequenced the exact same sample (within the space of 24 hours) using an ABI 3130 sanger sequencer to sequence a given region as well as by NGS analyses (Nextera PE on a nextseq 500). The sample was a lyophilized live attenuated vaccine (Highly passaged DNA double stranded virus)
To my surprise (and disappointment), the sequences don't match. I've attached a screenshot of the Sanger sequence aligned to the reference genome. There don't appear to be any peaks under peaks that suggest a heterogenous sample. I've also attached the mapped reads of the Illumina data, and there are no reads that contain the two variations seen in the Sanger data (images below)
Anyone have any idea about what could be going on?!
Thanks in advance