Thread by @emmecola

Question for bioinformaticians! Believe it or not, the first genome of bat virus #RaTG13 had some nucleotides that were supported by zero reads: in other words, the genome didn't match the sequences that were used to assemble it. How is it possible? 1/
#originsofSARSCoV2

Assemblers are computer programs, they do not "invent" nucleotides. So, what happened here? My explanation was that this genome was assembled using other reads, maybe in addition to the ones that were uploaded. 2/

In that case, I expected the authors to upload the missing reads.. Instead they did the opposite: they updated the genome, replacing the nucleotides supported by zero reads with the correct ones. So, the question is: how the heck did they assemble the genome the first time? 3/

Moreover, while they fixed the genome in those positions, at the same time they also added 15 brand new nucleotides at genome start, again with no support in the raw data. #Wuhan Institute of Virology: the place where magic happens! 4/

By the way, if you want to play with the data, you can start from the alignments published by @K_G_Andersen. Please let me know your results, as well as your explanations for these weird issues.. I am curious!
virological.org/t/on-the-verac…