84e8a21220c712339da59a4c53ed481162c64156 angie Fri Aug 26 12:00:07 2022 -0700 Add IDs for a bunch of new recombinants. diff --git src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv index 2d68321..173b72e 100644 --- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv +++ src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv @@ -159,186 +159,243 @@ England/MILK-3534D77/2022 445 XF England/MILK-3548B2B/2022 445 XF England/MILK-354CDB8/2022 445 XF England/MILK-355A151/2022 445 XF England/MILK-357D361/2022 445 XF England/MILK-358F302/2022 445 XF England/MILK-358F6AF/2022 445 XF England/MILK-359F008/2022 445 XF England/MILK-35A6CFB/2022 445 XF England/MILK-3602CCF/2022 445 XF England/MILK-365F003/2022 445 XF England/MILK-36E1AF9/2022 445 XF England/NORT-YB6X6S/2022 445 XF England/PHEC-YYN8J41/2022 445 XF England/PHEC-YYNR51S/2022 445 XF -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_8922263 447 XG +EPI_ISL_9010592 447 XG +EPI_ISL_9123271 447 XG +EPI_ISL_9127654 447 XG +EPI_ISL_9127907 447 XG +EPI_ISL_9128667 447 XG +EPI_ISL_9162908 447 XG +EPI_ISL_9166546 447 XG +EPI_ISL_9269735 447 XG +EPI_ISL_9270822 447 XG +EPI_ISL_9365440 447 XG +EPI_ISL_9365916 447 XG +EPI_ISL_9367129 447 XG +EPI_ISL_9410195 447 XG +EPI_ISL_9447008 447 XG +EPI_ISL_9564674 447 XG +EPI_ISL_9653239 447 XG +EPI_ISL_9653274 447 XG +EPI_ISL_9653281 447 XG +EPI_ISL_9654269 447 XG +EPI_ISL_9655126 447 XG +EPI_ISL_9691301 447 XG +EPI_ISL_9691377 447 XG +EPI_ISL_9691944 447 XG +EPI_ISL_9785347 447 XG +EPI_ISL_9855246 447 XG +EPI_ISL_9856140 447 XG +EPI_ISL_9856155 447 XG +EPI_ISL_9856373 447 XG +EPI_ISL_9856903 447 XG +EPI_ISL_9859266 447 XG +EPI_ISL_9859700 447 XG +EPI_ISL_9904514 447 XG +EPI_ISL_9972044 447 XG +EPI_ISL_9972435 447 XG +EPI_ISL_10011794 447 XG +EPI_ISL_10013280 447 XG +EPI_ISL_10015023 447 XG +EPI_ISL_10015592 447 XG +EPI_ISL_10061537 447 XG +EPI_ISL_10061733 447 XG +EPI_ISL_10064112 447 XG +EPI_ISL_10067433 447 XG +EPI_ISL_10093421 447 XG +EPI_ISL_10093473 447 XG +EPI_ISL_10093584 447 XG +EPI_ISL_10094142 447 XG +EPI_ISL_10094405 447 XG +EPI_ISL_10094657 447 XG +EPI_ISL_10095412 447 XG +EPI_ISL_10095522 447 XG +EPI_ISL_10095577 447 XG +EPI_ISL_10095630 447 XG +EPI_ISL_10203736 447 XG +EPI_ISL_10203572 447 XG +EPI_ISL_10203835 447 XG +EPI_ISL_10216164 447 XG +EPI_ISL_10209781 447 XG +EPI_ISL_10209717 447 XG +EPI_ISL_10258774 447 XG +EPI_ISL_10260270 447 XG +EPI_ISL_10252933 447 XG +EPI_ISL_10201743 447 XG +EPI_ISL_10259287 447 XG +EPI_ISL_10259103 447 XG +EPI_ISL_10318984 447 XG +EPI_ISL_10349122 447 XG +EPI_ISL_10349073 447 XG +EPI_ISL_10350127 447 XG +EPI_ISL_10350284 447 XG +EPI_ISL_10353954 447 XG +EPI_ISL_10353555 447 XG +EPI_ISL_10399175 447 XG +EPI_ISL_10399838 447 XG +EPI_ISL_10399954 447 XG +EPI_ISL_10399960 447 XG +EPI_ISL_10400070 447 XG +EPI_ISL_10400546 447 XG +EPI_ISL_10400577 447 XG +EPI_ISL_10012850 447 XG +EPI_ISL_10066606 447 XG +EPI_ISL_10253010 447 XG +EPI_ISL_10284531 447 XG +EPI_ISL_10317926 447 XG +EPI_ISL_10318568 447 XG +EPI_ISL_10349654 447 XG +EPI_ISL_10507630 447 XG +EPI_ISL_10509804 447 XG +EPI_ISL_10510819 447 XG +EPI_ISL_10510968 447 XG +EPI_ISL_10511619 447 XG +EPI_ISL_10532208 447 XG +EPI_ISL_10535975 447 XG +EPI_ISL_10581784 447 XG +EPI_ISL_10582143 447 XG +EPI_ISL_10582318 447 XG +EPI_ISL_10584075 447 XG +EPI_ISL_10584328 447 XG +EPI_ISL_10584366 447 XG +EPI_ISL_10585364 447 XG +EPI_ISL_10586509 447 XG +EPI_ISL_10586828 447 XG +Scotland/QEUH-37E04A0/2022 447 XG +England/MILK-3795589/2022 447 XG +EPI_ISL_8465919 448 XH +EPI_ISL_8702247 448 XH +EPI_ISL_8767403 448 XH +EPI_ISL_9065843 448 XH +EPI_ISL_9066877 448 XH +EPI_ISL_9064620 448 XH +EPI_ISL_9007989 448 XH +EPI_ISL_9010513 448 XH +EPI_ISL_9010917 448 XH +EPI_ISL_9120017 448 XH +EPI_ISL_9120205 448 XH +EPI_ISL_9126943 448 XH +EPI_ISL_8529537 448 XH +EPI_ISL_9163469 448 XH +EPI_ISL_8833007 448 XH +EPI_ISL_8833093 448 XH +EPI_ISL_9167531 448 XH +EPI_ISL_8887203 448 XH +EPI_ISL_8926995 448 XH +EPI_ISL_8925096 448 XH +EPI_ISL_9237843 448 XH +EPI_ISL_9238597 448 XH +EPI_ISL_9243151 448 XH +EPI_ISL_9238464 448 XH +EPI_ISL_9236009 448 XH +EPI_ISL_9270778 448 XH +EPI_ISL_9358935 448 XH +EPI_ISL_9358324 448 XH +EPI_ISL_9411270 448 XH +EPI_ISL_9454346 448 XH +EPI_ISL_9504399 448 XH +EPI_ISL_9495907 448 XH +EPI_ISL_9652491 448 XH +EPI_ISL_9653598 448 XH +EPI_ISL_9854699 448 XH +EPI_ISL_9855785 448 XH +EPI_ISL_9898451 448 XH +EPI_ISL_9904247 448 XH +EPI_ISL_9900944 448 XH +EPI_ISL_10064603 448 XH +EPI_ISL_10064569 448 XH +EPI_ISL_10095405 448 XH +EPI_ISL_9973212 449 XJ +EPI_ISL_10266422 449 XJ +EPI_ISL_10266423 449 XJ +EPI_ISL_10266424 449 XJ +EPI_ISL_10266425 449 XJ +EPI_ISL_10266426 449 XJ +EPI_ISL_10266427 449 XJ +EPI_ISL_10266428 449 XJ +EPI_ISL_10266429 449 XJ +EPI_ISL_10148532 449 XJ +EPI_ISL_10513491 449 XJ +EPI_ISL_10513717 449 XJ +EPI_ISL_10513762 449 XJ +EPI_ISL_10599971 449 XJ +EPI_ISL_10609794 449 XJ +EPI_ISL_10814640 449 XJ +EPI_ISL_10898591 449 XJ +EPI_ISL_10978544 449 XJ +EPI_ISL_11300500 449 XJ +EPI_ISL_11300501 449 XJ +EPI_ISL_11300502 449 XJ +EPI_ISL_11300503 449 XJ +EPI_ISL_11300504 449 XJ +EPI_ISL_11300505 449 XJ +EPI_ISL_11300506 449 XJ +EPI_ISL_11300507 449 XJ +EPI_ISL_11300508 449 XJ +EPI_ISL_11300509 449 XJ +EPI_ISL_11300510 449 XJ +EPI_ISL_11300511 449 XJ +EPI_ISL_11300512 449 XJ +EPI_ISL_11300513 449 XJ +EPI_ISL_11300514 449 XJ +EPI_ISL_11300515 449 XJ +EPI_ISL_11300516 449 XJ +EPI_ISL_11300517 449 XJ +EPI_ISL_11300518 449 XJ +EPI_ISL_11300519 449 XJ +EPI_ISL_11300520 449 XJ +EPI_ISL_11300521 449 XJ +EPI_ISL_11300522 449 XJ +EPI_ISL_11300523 449 XJ +EPI_ISL_11300524 449 XJ +EPI_ISL_11300525 449 XJ +EPI_ISL_11300526 449 XJ +EPI_ISL_11300527 449 XJ +EPI_ISL_11300528 449 XJ +EPI_ISL_11300529 449 XJ +EPI_ISL_11300530 449 XJ +EPI_ISL_11300531 449 XJ +EPI_ISL_11300532 449 XJ +EPI_ISL_11300533 449 XJ +EPI_ISL_11300534 449 XJ +EPI_ISL_11300535 449 XJ +EPI_ISL_11300536 449 XJ +EPI_ISL_11300537 449 XJ +EPI_ISL_11300538 449 XJ +EPI_ISL_11300539 449 XJ +EPI_ISL_11300540 449 XJ +EPI_ISL_11300541 449 XJ +EPI_ISL_11300542 449 XJ +EPI_ISL_11300543 449 XJ +EPI_ISL_11300544 449 XJ +EPI_ISL_11300545 449 XJ +EPI_ISL_11300546 449 XJ +EPI_ISL_11300547 449 XJ +England/MILK-393A26F/2022 449 XJ EPI_ISL_9118626 454 XE EPI_ISL_9177743 454 XE EPI_ISL_9317804 454 XE EPI_ISL_9360159 454 XE EPI_ISL_9374203 454 XE EPI_ISL_9442114 454 XE EPI_ISL_9561615 454 XE EPI_ISL_9640507 454 XE EPI_ISL_9640510 454 XE EPI_ISL_9680768 454 XE EPI_ISL_9685500 454 XE EPI_ISL_9723901 454 XE EPI_ISL_9724033 454 XE EPI_ISL_9726465 454 XE EPI_ISL_9778646 454 XE @@ -929,122 +986,132 @@ Scotland/QEUH-3832532/2022 454 XE Scotland/QEUH-383ABFC/2022 454 XE Scotland/QEUH-384D279/2022 454 XE Scotland/QEUH-38522BD/2022 454 XE Scotland/QEUH-385878B/2022 454 XE Scotland/QEUH-3858ADD/2022 454 XE Scotland/QEUH-3861664/2022 454 XE Scotland/QEUH-386178F/2022 454 XE Scotland/QEUH-3862A76/2022 454 XE Scotland/QEUH-386436A/2022 454 XE Scotland/QEUH-3866C8B/2022 454 XE Scotland/QEUH-3871AFC/2022 454 XE Scotland/QEUH-3871BCC/2022 454 XE Wales/PHWC-PEQPDX/2022 454 XE EPI_ISL_8402519 455 -EPI_ISL_10864854 460 -EPI_ISL_10864857 460 -EPI_ISL_10864858 460 -EPI_ISL_10864920 460 -EPI_ISL_10864921 460 -EPI_ISL_10864925 460 -EPI_ISL_10865165 460 -EPI_ISL_10892048 460 -EPI_ISL_10892049 460 -EPI_ISL_10892050 460 -EPI_ISL_10892051 460 -EPI_ISL_10892052 460 -EPI_ISL_10892053 460 -EPI_ISL_10892054 460 -EPI_ISL_11009573 460 -EPI_ISL_11009624 460 -EPI_ISL_11046434 460 -EPI_ISL_11046441 460 +EPI_ISL_10864854 460 XK +EPI_ISL_10864857 460 XK +EPI_ISL_10864858 460 XK +EPI_ISL_10864920 460 XK +EPI_ISL_10864921 460 XK +EPI_ISL_10864925 460 XK +EPI_ISL_10865165 460 XK +EPI_ISL_10892048 460 XK +EPI_ISL_10892049 460 XK +EPI_ISL_10892050 460 XK +EPI_ISL_10892051 460 XK +EPI_ISL_10892052 460 XK +EPI_ISL_10892053 460 XK +EPI_ISL_10892054 460 XK +EPI_ISL_11009573 460 XK +EPI_ISL_11009624 460 XK +EPI_ISL_11046434 460 XK +EPI_ISL_11046441 460 XK EPI_ISL_9653629 463 EPI_ISL_9653714 463 EPI_ISL_9788858 463 EPI_ISL_9859723 463 EPI_ISL_10064888 463 EPI_ISL_10094246 463 EPI_ISL_10205420 463 EPI_ISL_10210786 463 EPI_ISL_10352947 463 EPI_ISL_10633947 463 EPI_ISL_10634868 463 EPI_ISL_10677314 463 EPI_ISL_10732655 463 EPI_ISL_10807605 463 EPI_ISL_10809722 463 EPI_ISL_10810199 463 EPI_ISL_10811843 463 EPI_ISL_10859747 463 -EPI_ISL_9839483 464 -EPI_ISL_9839682 464 -EPI_ISL_9872878 464 -EPI_ISL_9894508 464 -EPI_ISL_10413150 464 -EPI_ISL_10413918 464 -EPI_ISL_10415682 464 -EPI_ISL_10480052 464 -EPI_ISL_10515444 464 -EPI_ISL_10537883 464 -EPI_ISL_10641197 464 -EPI_ISL_10688213 464 -EPI_ISL_10734696 464 -EPI_ISL_10736100 464 -EPI_ISL_10797107 464 -EPI_ISL_10799679 464 -EPI_ISL_10845598 464 -EPI_ISL_10884842 464 -EPI_ISL_10885820 464 -EPI_ISL_10885891 464 -EPI_ISL_10885898 464 -EPI_ISL_10885929 464 -EPI_ISL_10885983 464 -EPI_ISL_10886013 464 -EPI_ISL_10886093 464 -EPI_ISL_10932582 464 -EPI_ISL_10938170 464 -OV950637.1 464 -OV955312.1 464 -OV962278.1 464 -OV968185.1 464 -England/LSPA-37BF0E2/2022 464 -England/LSPA-37E113F/2022 464 -England/LSPA-387FD7D/2022 464 -England/LSPA-38BDD28/2022 464 -England/LSPA-38C0D04/2022 464 -England/MILK-35C3232/2022 464 -England/MILK-35C340F/2022 464 -England/MILK-35D54EC/2022 464 -England/MILK-360CAE9/2022 464 -England/MILK-3722ABF/2022 464 -England/MILK-37AA026/2022 464 -England/MILK-37DE1F9/2022 464 -England/MILK-3818BD6/2022 464 -England/MILK-385687B/2022 464 -England/MILK-38A23E8/2022 464 -England/MILK-38C9D1A/2022 464 -England/MILK-38EA180/2022 464 -England/MILK-38F4280/2022 464 -England/MILK-38FDD4A/2022 464 -England/MILK-38FF470/2022 464 -England/MILK-38FF48F/2022 464 -England/MILK-38FF4AD/2022 464 -England/MILK-38FF513/2022 464 -England/MILK-38FF59B/2022 464 -England/MILK-38FF6C5/2022 464 +EPI_ISL_10893424 463 +EPI_ISL_10981999 463 +EPI_ISL_10982953 463 +EPI_ISL_10983612 463 +EPI_ISL_11025935 463 +EPI_ISL_11026539 463 +EPI_ISL_11113211 463 +EPI_ISL_11159064 463 +EPI_ISL_11279679 463 +EPI_ISL_11286273 463 +EPI_ISL_9839483 464 XL +EPI_ISL_9839682 464 XL +EPI_ISL_9872878 464 XL +EPI_ISL_9894508 464 XL +EPI_ISL_10413150 464 XL +EPI_ISL_10413918 464 XL +EPI_ISL_10415682 464 XL +EPI_ISL_10480052 464 XL +EPI_ISL_10515444 464 XL +EPI_ISL_10537883 464 XL +EPI_ISL_10641197 464 XL +EPI_ISL_10688213 464 XL +EPI_ISL_10734696 464 XL +EPI_ISL_10736100 464 XL +EPI_ISL_10797107 464 XL +EPI_ISL_10799679 464 XL +EPI_ISL_10845598 464 XL +EPI_ISL_10884842 464 XL +EPI_ISL_10885820 464 XL +EPI_ISL_10885891 464 XL +EPI_ISL_10885898 464 XL +EPI_ISL_10885929 464 XL +EPI_ISL_10885983 464 XL +EPI_ISL_10886013 464 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