f488be28f1793410327aa93ac1ba01982b37f260 angie Sat Mar 12 20:34:27 2022 -0800 Adding lots of updates from pango-designation; also COG-UK names because not all are in GenBank downloads yet. diff --git src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv index b0d77a4..b3eb649 100644 --- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv +++ src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv @@ -1,490 +1,1241 @@ ID pango-designation issue number or comment England/ALDP-2F86D33/2021 422 England/QEUH-312A66E/2022 422 England/ALDP-31AE19E/2022 422 England/ALDP-325CFB2/2022 422 OV626513.1 422 OV628319.1 422 OV720067.1 422 OV721520.1 422 EPI_ISL_8166781 422 EPI_ISL_8610834 422 EPI_ISL_8865709 422 EPI_ISL_8898412 422 EPI_ISL_8438332 437 EPI_ISL_10262189 437 EPI_ISL_10263151 437 EPI_ISL_10263152 437 EPI_ISL_10261577 437 EPI_ISL_10305529 437 OM392955.1 439 OM393452.1 439 OM372355.1 439 OM344043.1 439 OM344166.1 439 OM344238.1 439 OM272834.1 439 EPI_ISL_8720194 439 EPI_ISL_8981459 439 EPI_ISL_8981712 439 EPI_ISL_8981824 439 EPI_ISL_9088187 439 EPI_ISL_9147438 439 EPI_ISL_9147935 439 England/PLYM-32FEF76/2022 441 England/PLYM-332E079/2022 441 England/PLYM-332E510/2022 441 England/PLYM-336A651/2022 441 England/PLYM-33BB5CD/2022 441 OV757286.1 441 OV758622.1 441 OV768982.1 441 OV781287.1 441 OV807225.1 441 EPI_ISL_9125312 441 EPI_ISL_9175215 441 EPI_ISL_9026013 441 EPI_ISL_9062592 441 EPI_ISL_9296739 441 EPI_ISL_9959921 444 EPI_ISL_9879437 444 EPI_ISL_9879436 444 EPI_ISL_9863764 444 EPI_ISL_9857381 444 EPI_ISL_9791275 444 EPI_ISL_9449070 444 EPI_ISL_9166910 444 EPI_ISL_9518370 444 EPI_ISL_9791300 444 EPI_ISL_10096770 444 EPI_ISL_10014373 444 EPI_ISL_10207240 444 EPI_ISL_10210832 444 EPI_ISL_10352397 444 EPI_ISL_10511379 444 EPI_ISL_10528736 444 EPI_ISL_10529499 444 EPI_ISL_10531214 444 EPI_ISL_10550896 444 EPI_ISL_10550897 444 EPI_ISL_10550898 444 EPI_ISL_10551446 444 EPI_ISL_10551447 444 EPI_ISL_10551448 444 EPI_ISL_8894978 445 EPI_ISL_8899193 445 EPI_ISL_8964736 445 EPI_ISL_9024950 445 EPI_ISL_9027096 445 EPI_ISL_9074902 445 EPI_ISL_9174471 445 EPI_ISL_9247732 445 EPI_ISL_9254198 445 EPI_ISL_9256573 445 EPI_ISL_9284798 445 EPI_ISL_9296126 445 EPI_ISL_9310093 445 EPI_ISL_9399416 445 EPI_ISL_9411495 445 EPI_ISL_9589270 445 EPI_ISL_9641789 445 EPI_ISL_9681404 445 EPI_ISL_9727711 445 EPI_ISL_9729847 445 EPI_ISL_9732451 445 EPI_ISL_9783055 445 EPI_ISL_9790074 445 EPI_ISL_9813122 445 EPI_ISL_9818970 445 EPI_ISL_9825890 445 EPI_ISL_9827103 445 EPI_ISL_9827194 445 EPI_ISL_9866660 445 EPI_ISL_9996515 445 EPI_ISL_10106252 445 EPI_ISL_10348464 445 EPI_ISL_10357090 445 EPI_ISL_10388349 445 OV720991.1 445 OV723571.1 445 OV738853.1 445 OV756288.1 445 OV758512.1 445 OV764698.1 445 OV780992.1 445 OV786378.1 445 OV787989.1 445 OV797151.1 445 OV802239.1 445 OV810231.1 445 OV826120.1 445 OV838244.1 445 OV895508.1 445 +OW002725.1 445 +OV903385.1 445 +OV925428.1 445 +OV926268.1 445 +OV927647.1 445 +OV935452.1 445 +OV940828.1 445 +OV941737.1 445 +OV950003.1 445 +OV940146.1 445 +OV940149.1 445 +OV953888.1 445 +OV992408.1 445 +England/DHSC-CYB1NDG/2022 445 +England/DHSC-CYBR1GP/2022 445 +England/DHSC-CYY89OG/2022 445 +England/HSLL-32DE9C9/2022 445 +England/HSLL-34107CF/2022 445 +England/HSLL-345C897/2022 445 +England/MILK-3251BB9/2022 445 +England/MILK-3270598/2022 445 +England/MILK-327F0C5/2022 445 +England/MILK-32A5DDE/2022 445 +England/MILK-32F2D5A/2022 445 +England/MILK-335FD3C/2022 445 +England/MILK-3387366/2022 445 +England/MILK-338970E/2022 445 +England/MILK-3394D0E/2022 445 +England/MILK-33A6C1B/2022 445 +England/MILK-33CD768/2022 445 +England/MILK-352138A/2022 445 +England/MILK-352B292/2022 445 +England/MILK-3534D77/2022 445 +England/MILK-3548B2B/2022 445 +England/MILK-354CDB8/2022 445 +England/MILK-355A151/2022 445 +England/MILK-357D361/2022 445 +England/MILK-358F302/2022 445 +England/MILK-358F6AF/2022 445 +England/MILK-359F008/2022 445 +England/MILK-35A6CFB/2022 445 +England/MILK-3602CCF/2022 445 +England/MILK-365F003/2022 445 +England/MILK-36E1AF9/2022 445 +England/NORT-YB6X6S/2022 445 +England/PHEC-YYN8J41/2022 445 +England/PHEC-YYNR51S/2022 445 EPI_ISL_8922263 447 EPI_ISL_9010592 447 EPI_ISL_9123271 447 EPI_ISL_9127654 447 EPI_ISL_9127907 447 EPI_ISL_9128667 447 EPI_ISL_9162908 447 EPI_ISL_9166546 447 EPI_ISL_9269735 447 EPI_ISL_9270822 447 EPI_ISL_9365440 447 EPI_ISL_9365916 447 EPI_ISL_9367129 447 EPI_ISL_9410195 447 EPI_ISL_9447008 447 EPI_ISL_9564674 447 EPI_ISL_9653239 447 EPI_ISL_9653274 447 EPI_ISL_9653281 447 EPI_ISL_9654269 447 EPI_ISL_9655126 447 EPI_ISL_9691301 447 EPI_ISL_9691377 447 EPI_ISL_9691944 447 EPI_ISL_9785347 447 EPI_ISL_9855246 447 EPI_ISL_9856140 447 EPI_ISL_9856155 447 EPI_ISL_9856373 447 EPI_ISL_9856903 447 EPI_ISL_9859266 447 EPI_ISL_9859700 447 EPI_ISL_9904514 447 EPI_ISL_9972044 447 EPI_ISL_9972435 447 EPI_ISL_10011794 447 EPI_ISL_10013280 447 EPI_ISL_10015023 447 EPI_ISL_10015592 447 EPI_ISL_10061537 447 EPI_ISL_10061733 447 EPI_ISL_10064112 447 EPI_ISL_10067433 447 EPI_ISL_10093421 447 EPI_ISL_10093473 447 EPI_ISL_10093584 447 EPI_ISL_10094142 447 EPI_ISL_10094405 447 EPI_ISL_10094657 447 EPI_ISL_10095412 447 EPI_ISL_10095522 447 EPI_ISL_10095577 447 EPI_ISL_10095630 447 EPI_ISL_10203736 447 EPI_ISL_10203572 447 EPI_ISL_10203835 447 EPI_ISL_10216164 447 EPI_ISL_10209781 447 EPI_ISL_10209717 447 EPI_ISL_10258774 447 EPI_ISL_10260270 447 EPI_ISL_10252933 447 EPI_ISL_10201743 447 EPI_ISL_10259287 447 EPI_ISL_10259103 447 EPI_ISL_10318984 447 EPI_ISL_10349122 447 EPI_ISL_10349073 447 EPI_ISL_10350127 447 EPI_ISL_10350284 447 EPI_ISL_10353954 447 EPI_ISL_10353555 447 EPI_ISL_10399175 447 EPI_ISL_10399838 447 EPI_ISL_10399954 447 EPI_ISL_10399960 447 EPI_ISL_10400070 447 EPI_ISL_10400546 447 EPI_ISL_10400577 447 EPI_ISL_10012850 447 EPI_ISL_10066606 447 EPI_ISL_10253010 447 EPI_ISL_10284531 447 EPI_ISL_10317926 447 EPI_ISL_10318568 447 EPI_ISL_10349654 447 EPI_ISL_10507630 447 EPI_ISL_10509804 447 EPI_ISL_10510819 447 EPI_ISL_10510968 447 EPI_ISL_10511619 447 EPI_ISL_10532208 447 EPI_ISL_10535975 447 EPI_ISL_10581784 447 EPI_ISL_10582143 447 EPI_ISL_10582318 447 EPI_ISL_10584075 447 EPI_ISL_10584328 447 EPI_ISL_10584366 447 EPI_ISL_10585364 447 EPI_ISL_10586509 447 EPI_ISL_10586828 447 +Scotland/QEUH-37E04A0/2022 447 +England/MILK-3795589/2022 447 EPI_ISL_8465919 448 EPI_ISL_8702247 448 EPI_ISL_8767403 448 EPI_ISL_9065843 448 EPI_ISL_9066877 448 EPI_ISL_9064620 448 EPI_ISL_9007989 448 EPI_ISL_9010513 448 EPI_ISL_9010917 448 EPI_ISL_9120017 448 EPI_ISL_9120205 448 EPI_ISL_9126943 448 EPI_ISL_8529537 448 EPI_ISL_9163469 448 EPI_ISL_8833007 448 EPI_ISL_8833093 448 EPI_ISL_9167531 448 EPI_ISL_8887203 448 EPI_ISL_8926995 448 EPI_ISL_8925096 448 EPI_ISL_9237843 448 EPI_ISL_9238597 448 EPI_ISL_9243151 448 EPI_ISL_9238464 448 EPI_ISL_9236009 448 EPI_ISL_9270778 448 EPI_ISL_9358935 448 EPI_ISL_9358324 448 EPI_ISL_9411270 448 EPI_ISL_9454346 448 EPI_ISL_9504399 448 EPI_ISL_9495907 448 EPI_ISL_9652491 448 EPI_ISL_9653598 448 EPI_ISL_9854699 448 EPI_ISL_9855785 448 EPI_ISL_9898451 448 EPI_ISL_9904247 448 EPI_ISL_9900944 448 EPI_ISL_10064603 448 EPI_ISL_10064569 448 EPI_ISL_10095405 448 EPI_ISL_9973212 449 EPI_ISL_10266422 449 EPI_ISL_10266423 449 EPI_ISL_10266424 449 EPI_ISL_10266425 449 EPI_ISL_10266426 449 EPI_ISL_10266427 449 EPI_ISL_10266428 449 EPI_ISL_10266429 449 EPI_ISL_10148532 449 EPI_ISL_9118626 454 EPI_ISL_9177743 454 EPI_ISL_9317804 454 EPI_ISL_9360159 454 EPI_ISL_9374203 454 EPI_ISL_9442114 454 EPI_ISL_9561615 454 EPI_ISL_9640507 454 EPI_ISL_9640510 454 EPI_ISL_9680768 454 EPI_ISL_9685500 454 EPI_ISL_9723901 454 EPI_ISL_9724033 454 EPI_ISL_9726465 454 EPI_ISL_9778646 454 EPI_ISL_9780750 454 EPI_ISL_9785535 454 EPI_ISL_9789810 454 EPI_ISL_9837985 454 EPI_ISL_9839163 454 EPI_ISL_9841256 454 EPI_ISL_9865436 454 EPI_ISL_9865927 454 EPI_ISL_9866059 454 EPI_ISL_9867133 454 EPI_ISL_9871599 454 EPI_ISL_9874224 454 EPI_ISL_9875444 454 EPI_ISL_9888391 454 EPI_ISL_9888437 454 EPI_ISL_9890728 454 EPI_ISL_9891687 454 EPI_ISL_9894676 454 EPI_ISL_9896755 454 EPI_ISL_9991191 454 EPI_ISL_9991839 454 EPI_ISL_9992095 454 EPI_ISL_9993159 454 EPI_ISL_9993289 454 EPI_ISL_9995887 454 EPI_ISL_9996009 454 EPI_ISL_9996395 454 EPI_ISL_9998424 454 EPI_ISL_9316611 454 EPI_ISL_9386983 454 EPI_ISL_9641769 454 EPI_ISL_9642613 454 EPI_ISL_9781137 454 EPI_ISL_9827934 454 EPI_ISL_9839903 454 EPI_ISL_9840058 454 EPI_ISL_9840129 454 EPI_ISL_9991932 454 EPI_ISL_9995284 454 EPI_ISL_10004232 454 EPI_ISL_10035165 454 EPI_ISL_10048837 454 EPI_ISL_10049744 454 EPI_ISL_10055032 454 EPI_ISL_10055800 454 EPI_ISL_10056125 454 EPI_ISL_10057698 454 EPI_ISL_10057718 454 EPI_ISL_10106431 454 EPI_ISL_10106439 454 EPI_ISL_10106478 454 EPI_ISL_10108218 454 EPI_ISL_10109693 454 EPI_ISL_10112261 454 EPI_ISL_10112394 454 EPI_ISL_10112876 454 EPI_ISL_10113327 454 EPI_ISL_10113552 454 EPI_ISL_10119827 454 EPI_ISL_10125100 454 EPI_ISL_10181370 454 EPI_ISL_10192281 454 EPI_ISL_10192418 454 EPI_ISL_10193674 454 EPI_ISL_10196334 454 EPI_ISL_10198019 454 EPI_ISL_10198363 454 EPI_ISL_10198524 454 EPI_ISL_10200051 454 EPI_ISL_10242764 454 EPI_ISL_10243273 454 EPI_ISL_10243417 454 EPI_ISL_10243480 454 EPI_ISL_10243794 454 EPI_ISL_10244013 454 EPI_ISL_10245193 454 EPI_ISL_10245373 454 EPI_ISL_10245469 454 EPI_ISL_10245618 454 EPI_ISL_10245701 454 EPI_ISL_10245725 454 EPI_ISL_10245766 454 EPI_ISL_10246087 454 EPI_ISL_10246410 454 EPI_ISL_10284540 454 EPI_ISL_10284555 454 EPI_ISL_10284600 454 EPI_ISL_10284865 454 EPI_ISL_10286915 454 EPI_ISL_10287255 454 EPI_ISL_10287386 454 EPI_ISL_10287399 454 EPI_ISL_10336103 454 EPI_ISL_10338741 454 EPI_ISL_10339410 454 EPI_ISL_10413007 454 EPI_ISL_10413008 454 EPI_ISL_10413156 454 EPI_ISL_10413868 454 EPI_ISL_10413976 454 EPI_ISL_10414620 454 EPI_ISL_10414913 454 EPI_ISL_10415414 454 EPI_ISL_10415563 454 EPI_ISL_10416799 454 EPI_ISL_10417379 454 EPI_ISL_10417433 454 EPI_ISL_10417482 454 EPI_ISL_10417546 454 EPI_ISL_10417598 454 EPI_ISL_10417663 454 EPI_ISL_10418744 454 EPI_ISL_10422361 454 EPI_ISL_10424931 454 EPI_ISL_10425271 454 EPI_ISL_10425759 454 EPI_ISL_10426230 454 EPI_ISL_10427588 454 EPI_ISL_10428495 454 EPI_ISL_10428969 454 EPI_ISL_10436801 454 EPI_ISL_10453987 454 EPI_ISL_10454010 454 EPI_ISL_10454071 454 EPI_ISL_10461587 454 EPI_ISL_10463221 454 EPI_ISL_10463311 454 EPI_ISL_10463579 454 EPI_ISL_10463690 454 EPI_ISL_10463709 454 EPI_ISL_10463872 454 EPI_ISL_10464667 454 EPI_ISL_10466511 454 EPI_ISL_10471384 454 EPI_ISL_10473104 454 EPI_ISL_10473814 454 EPI_ISL_10474531 454 EPI_ISL_10477146 454 EPI_ISL_10482059 454 EPI_ISL_10484416 454 EPI_ISL_10488502 454 EPI_ISL_10053482 454 EPI_ISL_10119815 454 EPI_ISL_10194351 454 EPI_ISL_10195082 454 EPI_ISL_10198019 454 EPI_ISL_10198524 454 EPI_ISL_10198019 454 EPI_ISL_10198524 454 EPI_ISL_10428288 454 EPI_ISL_10512719 454 EPI_ISL_10512745 454 EPI_ISL_10512733 454 EPI_ISL_10513213 454 EPI_ISL_10513800 454 EPI_ISL_10515356 454 EPI_ISL_10516813 454 EPI_ISL_10516604 454 EPI_ISL_10517482 454 EPI_ISL_10514194 454 EPI_ISL_10517633 454 EPI_ISL_10518473 454 EPI_ISL_10518752 454 EPI_ISL_10518819 454 EPI_ISL_10518005 454 EPI_ISL_10519525 454 EPI_ISL_10522124 454 EPI_ISL_10522380 454 EPI_ISL_10524361 454 EPI_ISL_10526979 454 EPI_ISL_10525794 454 EPI_ISL_10529916 454 EPI_ISL_10529632 454 EPI_ISL_10532829 454 EPI_ISL_10534022 454 EPI_ISL_10536130 454 EPI_ISL_10536356 454 EPI_ISL_10536641 454 EPI_ISL_10543255 454 EPI_ISL_10543335 454 EPI_ISL_10543210 454 +EPI_ISL_10571356 454 +EPI_ISL_10571556 454 +EPI_ISL_10572403 454 +EPI_ISL_10572026 454 +EPI_ISL_10572303 454 +EPI_ISL_10573300 454 +EPI_ISL_10572961 454 +EPI_ISL_10573739 454 +EPI_ISL_10577013 454 +EPI_ISL_10577893 454 +EPI_ISL_10587743 454 +EPI_ISL_10641307 454 +EPI_ISL_10641018 454 +EPI_ISL_10641104 454 +EPI_ISL_10642075 454 +EPI_ISL_10642606 454 +EPI_ISL_10642086 454 +EPI_ISL_10642839 454 +EPI_ISL_10641407 454 +EPI_ISL_10644123 454 +EPI_ISL_10644235 454 +EPI_ISL_10644417 454 +EPI_ISL_10644301 454 +EPI_ISL_10645019 454 +EPI_ISL_10644772 454 +EPI_ISL_10693449 454 +EPI_ISL_10684963 454 +EPI_ISL_10692778 454 +EPI_ISL_10691625 454 +EPI_ISL_10690325 454 +EPI_ISL_10690472 454 +EPI_ISL_10688409 454 +EPI_ISL_10687780 454 +EPI_ISL_10687912 454 +EPI_ISL_10686988 454 +EPI_ISL_10685466 454 +EPI_ISL_10686988 454 +EPI_ISL_10687780 454 +EPI_ISL_10687912 454 +EPI_ISL_10688409 454 +EPI_ISL_10690325 454 +EPI_ISL_10690472 454 +EPI_ISL_10691625 454 +EPI_ISL_10692778 454 +EPI_ISL_10693449 454 +EPI_ISL_10709177 454 +EPI_ISL_10709266 454 +EPI_ISL_10709473 454 +EPI_ISL_10710593 454 +EPI_ISL_10710931 454 +EPI_ISL_10724970 454 +EPI_ISL_10725219 454 +EPI_ISL_10726035 454 +EPI_ISL_10726070 454 +EPI_ISL_10726698 454 +EPI_ISL_10726809 454 +EPI_ISL_10726860 454 +EPI_ISL_10727061 454 +EPI_ISL_10727238 454 +EPI_ISL_10727503 454 +EPI_ISL_10727735 454 +EPI_ISL_10728213 454 +EPI_ISL_10735172 454 +EPI_ISL_10735405 454 +EPI_ISL_10735567 454 +EPI_ISL_10735574 454 +EPI_ISL_10735640 454 +EPI_ISL_10735792 454 +EPI_ISL_10735810 454 +EPI_ISL_10736184 454 +EPI_ISL_10743190 454 +EPI_ISL_10744048 454 +EPI_ISL_10762397 454 +EPI_ISL_10765989 454 +EPI_ISL_10768829 454 +EPI_ISL_10768945 454 OV774910.1 454 OV783131.1 454 OV815899.1 454 OV818161.1 454 OV822541.1 454 OV840742.1 454 OV869399.1 454 OV894188.1 454 OV894331.1 454 OV814889.1 454 OV835795.1 454 OV895377.1 454 OV896176.1 454 OV934572.1 454 OV946413.1 454 OV954492.1 454 OV954666.1 454 OV954832.1 454 +OV981657.1 454 +OV995648.1 454 +OV996520.1 454 +OV998429.1 454 +OV999303.1 454 +OV999440.1 454 +OV999598.1 454 +OW000609.1 454 +OW000575.1 454 +OW002064.1 454 +OW002858.1 454 +OW002074.1 454 +OW003555.1 454 +OW006267.1 454 +OW008633.1 454 +OW009089.1 454 +OW008497.1 454 +OW009576.1 454 +OW009702.1 454 +OW011458.1 454 +OW011396.1 454 +OW012449.1 454 +OW011934.1 454 +OW014413.1 454 +OW013631.1 454 +OW014939.1 454 +OW018082.1 454 +OW018356.1 454 +OW022422.1 454 +OW018845.1 454 +OW020187.1 454 +OW017741.1 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