@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @franciscodeasis @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant 1/ Interesting question. Others would start asking about 4991 -- another group virtually simultaneously pegged it was likely candidate for nearest relative to SARS-2 based on short RdRp fragment previously uploaded. They'd say, what about the other 29.5kb? They'd wonder if 4991
@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @franciscodeasis @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant 2/ was in fact SARS-2, give or take a few mutations. They'd then read the 4991 paper very closely and (even w/out SZ's out-of-school comments in the Sci Am profile) follow the same breadcrumbs we followed leading them to the mine deaths.
@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @franciscodeasis @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant 3/ Then what? Everybody would be demanding to know what happened with the miners, was that already COVID-19 & what happened with the 4991 sample they took back to Wuhan? They'd demand every bit of the history in minute detail. When you think about it that way, makes more sense...
@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @franciscodeasis @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant 4/ Hiding it would cause a boatload of problems. As it is, quietly releasing the whole sequence keeps thing from boiling over. And, although I don't think this is likely, there are ways you could make that sequence more "innocent" (less SARS-2-like) if you really wanted to...
@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @franciscodeasis @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant On the latter, low-quality sequence based on a small RNA sample stored 7 yrs in a -80 *might* include a lot of low-confidence base calls that would potentially artifactually reduce the top-line % sequence identity with SARS-2. Just a thought -- by no means saying it happened.
@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @franciscodeasis @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant It would definitely be interesting if someone who really knew this HTS pipeline stuff could put together a sequence with per-base confidence scores to get a better idea of how trustworthy that sequence (and hence the %identity) really is.
@BahulikarRahul @Daoyu15 @AntGDuarte @babarlelephant @TheSeeker268 @BillyBostickson @PaulGodolphin @BioObject @JJ2000426 @Nomdeplumi1 @_coltseavers @scottburke777 @still_a_nerd @jjcouey @Harvard2H @ydeigin @franciscodeasis @uacjess @CarltheChippy @DefeatTheElites @ico_dna @Real_Adam_B @nerdhaspower @RolandBakerIII @DrAntoniSerraT1 @babarelephant When this kind of assembly is done, do people use priors based on reference sequences to "tiebreak" base calls that would create "suspect" stop codons? Because, if the algorithm is prior-less on that account, that puts a limit on how unreliable the finished sequence can be.
