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farhat-lab / gentb-site

The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
https://gentb.hms.harvard.edu
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Mutation table on GenTB - Map shows the same letter in two columns #248

Closed mgro closed 2 years ago

mgro commented 3 years ago

The aaref and aavar columns are showing the same amino acid letters. See highlighted in screenshot

Screen Shot 2021-06-10 at 11 27 22 AM

doctormo commented 2 years ago

Of 780,936 mutations in the database, 12,490 has the same aaref and aavar of these, 9,848 could be fixed by setting the aaref correctly from it's stored reference codon. The remaining 2601 are synonymous and 41 of them were INDEL types with the same nucleotides.

There was no known location for import errors, this is likely input data gone wrong.

Can you confirm the data is now fixed on live?

mgro commented 2 years ago

Yes, I can confirm this is fixed. Thank you!

From: Martin Owens @.> Date: Monday, 4. October 2021 at 18:27 To: farhat-lab/gentb-site @.> Cc: Groeschel, Matthias @.>, Author @.> Subject: Re: [farhat-lab/gentb-site] Mutation table on GenTB - Map shows the same letter in two columns (#248)

Of 780,936 mutations in the database, 12,490 has the same aaref and aavar of these, 9,848 could be fixed by setting the aaref correctly from it's stored reference codon. The remaining 2601 are synonymous and 41 of them were INDEL types with the same nucleotides.

There was no known location for import errors, this is likely input data gone wrong.

Can you confirm the data is now fixed on live?

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