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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Two differents recombinants lineage for XU in lineages.csv #646

Closed sanschiffre closed 2 years ago

sanschiffre commented 2 years ago

Lineages.csv containt 7 XU samples :

Japan/IC-4679/2022,XU India/RJ-SMS-ICMR-INSACOG-TS-11049/2022,XU India/RJ-SMS-ICMR-INSACOG-TS-9433/2022,XU India/RJ-SMS-ICMR-INSACOG-TS-9434/2022,XU India/MH-KasturbaMCGM-ICMR-INSACOG-WG3595/2022,XU India/MH-KasturbaMCGM-ICMR-INSACOG-WG3600/2022,XU Australia/NSW-ICPMR-23049/2022,XU

But when you analysed them with Sc2rf, you can see that they are two differents lineages : Capture d’écran de 2022-05-17 09-40-01 India/RJ-SMS-ICMR-INSACOG-TS-11049/2022 has a breakpoint between 12880 and 13195 The six others have their breakpoint between 5386 and 8393

AngieHinrichs commented 2 years ago

Good catch @sanschiffre! I think it should be India/RJ-SMS-ICMR-INSACOG-TS-11440/2022 (EPI_ISL_10924169) instead of India/RJ-SMS-ICMR-INSACOG-TS-11049/2022 -- I suspect that was a copy-paste error in the original post for #522, where the tree screenshot shows RJ-SMS-ICMR-INSACOG-TS-11440 but the table of samples has -11049.

Chris is on holiday so I will make that change in lineages.csv.