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 @@ -108,30 +108,77 @@ 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 @@ -210,30 +257,32 @@ 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 @@ -458,33 +507,735 @@ 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 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+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 +OW017741.1 454 +OW017412.1 454 +OW016367.1 454 +OW016842.1 454 +OW016407.1 454 +OW021217.1 454 +OW021554.1 454 +OW016455.1 454 +OW021599.1 454 +OW012857.1 454 +OW023014.1 454 +OV901986.1 454 +OV909153.1 454 +OV923098.1 454 +OV923955.1 454 +OV925123.1 454 +OV932710.1 454 +OV933811.1 454 +OV936169.1 454 +OV940327.1 454 +OV946677.1 454 +OV951106.1 454 +OV954796.1 454 +OV957406.1 454 +OV937008.1 454 +OV937528.1 454 +OV952921.1 454 +OV959975.1 454 +OV961564.1 454 +OV962471.1 454 +OV962724.1 454 +OV963078.1 454 +OV965506.1 454 +OV965701.1 454 +OV968863.1 454 +OV971069.1 454 +OV984065.1 454 +OV983774.1 454 +OV984700.1 454 +OV984783.1 454 +OV985973.1 454 +OV985674.1 454 +OV991313.1 454 +OV991613.1 454 +OV991608.1 454 +OV992913.1 454 +OV975204.1 454 +England/ALDP-36F844C/2022 454 +England/ALDP-3783515/2022 454 +England/ARCH-002761B3/2022 454 +England/BRBR-3891B99/2022 454 +England/BRBR-389927E/2022 454 +England/BRBR-3899BBF/2022 454 +England/BRBR-3899D04/2022 454 +England/BRBR-389EF72/2022 454 +England/DHSC-CYBTMZS/2022 454 +England/DHSC-CYBUNJA/2022 454 +England/DHSC-CYDBKJU/2022 454 +England/DHSC-CYNNZ9A/2022 454 +England/HSLL-3635540/2022 454 +England/HSLL-3648B75/2022 454 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