# Information about the mutations distinguishing the B.1.1.7, B.1.351, P.1, and P.2 lineages from their parent lineages. # # Notes: # - ORF, CodonStartPos, etc. classify mutations according to our NCBI annotations. # - Fields beginning with New_ classify mutations according to our proposed reference gene set. POS ID REF ALT ORF CodonStartPos RefAA AltAA AAPOS AAID VariantType BLOSUM62 Conserved NonsynonymousRate SynonymousRate PValue InSCE CodAlignView UCSCview New_ORF New_CodonStartPos New_RefAA New_AltAA New_AAPOS New_AAID New_VariantType New_BLOSUM62 New_Conserved New_CodAlignView Lineages LineageNotes Notes 100 C100T C T Noncoding =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;99;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C100T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:43-159&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") Noncoding =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;99;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C100T", "CodAlignView") P.2 174 G174T G T Noncoding =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;173;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G174T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:117-233&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") Noncoding =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;173;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G174T", "CodAlignView") B.1.351 733 T733C T C orf1ab 731 D D 156 orf1ab:D156D Synonymous 0.383709772887 0.287530511666 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;732;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=T733C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:674-790&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 731 D D 156 orf1ab:D156D Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;732;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=T733C", "CodAlignView") P.1 913 C913T C T orf1ab 911 S S 216 orf1ab:S216S Synonymous 1.19123795953 0.772662217967 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;912;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C913T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:854-970&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 911 S S 216 orf1ab:S216S Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;912;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C913T", "CodAlignView") B.1.1.7 1059 C1059T C T orf1ab 1058 T I 265 orf1ab:T265I Radical -1 1.23337169601 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;1058;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C1059T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:1001-1117&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 1058 T I 265 orf1ab:T265I Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;1058;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C1059T", "CodAlignView") B.1.351 2692 A2692T A T orf1ab 2690 T T 809 orf1ab:T809T Synonymous 0.259377631037 0.11474929648 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;2691;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++T'@-59&f=A2692T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:2633-2749&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 2690 T T 809 orf1ab:T809T Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;2691;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++T'@-59&f=A2692T", "CodAlignView") B.1.351 Not fixed in B.1.351. 2749 C2749T C T orf1ab 2747 D D 828 orf1ab:D828D Synonymous 1.74868319746 0.403461680362 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;2748;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C2749T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:2690-2806&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 2747 D D 828 orf1ab:D828D Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;2748;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C2749T", "CodAlignView") P.1 3267 C3267T C T orf1ab 3266 T I 1001 orf1ab:T1001I Radical -1 102.43669204 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;3266;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C3267T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:3209-3325&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 3266 T I 1001 orf1ab:T1001I Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;3266;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C3267T", "CodAlignView") B.1.1.7 3828 C3828T C T orf1ab 3827 S L 1188 orf1ab:S1188L Radical -2 8.52995066274 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;3827;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C3828T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:3770-3886&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 3827 S L 1188 orf1ab:S1188L Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;3827;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C3828T", "CodAlignView") P.1 5230 G5230T G T orf1ab 5228 K N 1655 orf1ab:K1655N Radical 0 1.24804700755 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5229;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G5230T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:5171-5287&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 5228 K N 1655 orf1ab:K1655N Radical 0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5229;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G5230T", "CodAlignView") B.1.351 5388 C5388A C A orf1ab 5387 A D 1708 orf1ab:A1708D Radical -2 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5387;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C5388A", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:5330-5446&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 5387 A D 1708 orf1ab:A1708D Radical -2 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5387;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C5388A", "CodAlignView") B.1.1.7 Radical amino acid change in string of 7 perfectly conserved amino acids, in well-conserved region of nsp3. 5648 A5648C A C orf1ab 5648 K Q 1795 orf1ab:K1795Q Conservative 1 1.87791201492 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5647;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=A5648C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:5591-5707&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 5648 K Q 1795 orf1ab:K1795Q Conservative 1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5647;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=A5648C", "CodAlignView") P.1 5986 C5986T C T orf1ab 5984 F F 1907 orf1ab:F1907F Synonymous 0.896693817735 0.852599283236 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5985;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C5986T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:5927-6043&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 5984 F F 1907 orf1ab:F1907F Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;5985;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C5986T", "CodAlignView") B.1.1.7 6319 A6319G A G orf1ab 6317 P P 2018 orf1ab:P2018P Synonymous 1.1326713196 0.827294735187 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;6318;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=A6319G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:6260-6376&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 6317 P P 2018 orf1ab:P2018P Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;6318;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=A6319G", "CodAlignView") P.1 6613 A6613G A G orf1ab 6611 V V 2116 orf1ab:V2116V Synonymous 0.824932035282 0.728194938158 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;6612;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=A6613G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:6554-6670&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 6611 V V 2116 orf1ab:V2116V Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;6612;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=A6613G", "CodAlignView") P.1 6954 T6954C T C orf1ab 6953 I T 2230 orf1ab:I2230T Radical -1 5.99039475006 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;6953;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=T6954C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:6896-7012&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 6953 I T 2230 orf1ab:I2230T Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;6953;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=T6954C", "CodAlignView") B.1.1.7 8660 C8660T C T orf1ab 8660 H Y 2799 orf1ab:H2799Y Conservative 2 1.34670291945 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;8659;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C8660T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:8603-8719&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 8660 H Y 2799 orf1ab:H2799Y Conservative 2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;8659;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C8660T", "CodAlignView") B.1.351 Not fixed in B.1.351. 8964 C8964T C T orf1ab 8963 S L 2900 orf1ab:S2900L Radical -2 1.47210524354 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;8963;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C8964T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:8906-9022&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 8963 S L 2900 orf1ab:S2900L Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;8963;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C8964T", "CodAlignView") B.1.351 Not fixed in B.1.351. 10323 A10323G A G orf1ab 10322 K R 3353 orf1ab:K3353R Conservative 2 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;10322;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A10323G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:10265-10381&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 10322 K R 3353 orf1ab:K3353R Conservative 2 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;10322;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A10323G", "CodAlignView") B.1.351 Conservative amino acid change in a moderately conserved region of 3CLpro. 10667 T10667G T G orf1ab 10667 L V 3468 orf1ab:L3468V Conservative 1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;10666;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=T10667G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:10610-10726&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 10667 L V 3468 orf1ab:L3468V Conservative 1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;10666;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=T10667G", "CodAlignView") P.2 Conservative amino acid change in highly conserved region of 3CLpro (13 amino acids with 0 changes; 44 amino acids with two conservative changes and no radical ones). 11288 11288-11296 deletion orf1ab 11288 3675 orf1ab:del3675-3677 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;11287;9;0&p=54&e=45&w=0&cp=0&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++---------+++++++++++++++++++++++++++++++++++++++++++++'@-54&f=11288-11296%20del", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:11234-11341&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 11288 3675 orf1ab:del3675-3677 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;11287;9;0&p=54&e=45&w=0&cp=0&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++---------+++++++++++++++++++++++++++++++++++++++++++++'@-54&f=11288-11296%20del", "CodAlignView") B.1.1.7 Two of the three deleted amino acids are perfectly conserved and the other just has one conservative amino acid change. It is in a string of 16 amino acids with no radical amino acid changes, only one of which has conservative changes. 11824 C11824T C T orf1ab 11822 I I 3853 orf1ab:I3853I Synonymous 1.36836565656 0.510970045909 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;11823;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C11824T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:11765-11881&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 11822 I I 3853 orf1ab:I3853I Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;11823;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C11824T", "CodAlignView") P.2 12053 C12053T C T orf1ab 12053 L F 3930 orf1ab:L3930F Radical 0 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;12052;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C12053T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:11996-12112&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 12053 L F 3930 orf1ab:L3930F Radical 0 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;12052;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C12053T", "CodAlignView") P.2 Radical amino acid change in long generally well-conserved section of nsp7. Only one radical amino acid substitution in one strain within 20 codons in either direction. 12778 C12778T C T orf1ab 12776 Y Y 4171 orf1ab:Y4171Y Synonymous 0.634679539255 0.456407740966 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;12777;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C12778T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:12719-12835&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 12776 Y Y 4171 orf1ab:Y4171Y Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;12777;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C12778T", "CodAlignView") P.1 13843 G13843T G T orf1ab 13843 D Y 4527 orf1ab:D4527Y Radical -3 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;13842;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++'@-57&f=G13843T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:13786-13902&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 13843 D Y 4527 orf1ab:D4527Y Radical -3 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;13842;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++'@-57&f=G13843T", "CodAlignView") B.1.351 Not fixed in B.1.351. Radical change in a string of 33 perfectly conserved amino acids in RdRp. 13860 C13860T C T orf1ab 13858 D D 4532 orf1ab:D4532D Synonymous 7.01144605259 0.000454466680674 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;13859;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C13860T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:13801-13917&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 13858 D D 4532 orf1ab:D4532D Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;13859;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C13860T", "CodAlignView") P.1 14676 C14676T C T orf1ab 14674 P P 4804 orf1ab:P4804P Synonymous Conserved 0.154913127574 0.00810533674817 InSCE =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;14675;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C14676T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:14617-14733&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 14674 P P 4804 orf1ab:P4804P Synonymous Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;14675;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C14676T", "CodAlignView") B.1.1.7 In RdRp. Unusually large SCE (25-codons long), with two others nearby, making a synonymously-constrained region around 200 nt long. Synonymously-constrained even relative to the rest of RdRp. 14925 C14925T C T orf1ab 14923 V V 4887 orf1ab:V4887V Synonymous 0.511341917073 0.35654557639 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;14924;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C14925T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:14866-14982&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 14923 V V 4887 orf1ab:V4887V Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;14924;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C14925T", "CodAlignView") B.1.351 Not fixed in B.1.351. 15279 C15279T C T orf1ab 15277 H H 5005 orf1ab:H5005H Synonymous 0.308138392495 0.0632232581193 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;15278;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C15279T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:15220-15336&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 15277 H H 5005 orf1ab:H5005H Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;15278;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C15279T", "CodAlignView") B.1.1.7 16176 T16176C T C orf1ab 16174 T T 5304 orf1ab:T5304T Synonymous 1.0886885563 0.867154192362 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;16175;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=T16176C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:16117-16233&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 16174 T T 5304 orf1ab:T5304T Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;16175;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=T16176C", "CodAlignView") B.1.1.7 17259 G17259T G T orf1ab 17257 E D 5665 orf1ab:E5665D Conservative 2 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;17258;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G17259T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:17200-17316&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 17257 E D 5665 orf1ab:E5665D Conservative 2 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;17258;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G17259T", "CodAlignView") P.1 Conservative amino acid change in extremely well-conserved region of Hel (86 amino acids with no changes in 42 of the 44 strains, and only 4 changes in those strains). 17999 C17999T C T orf1ab 17998 T I 5912 orf1ab:T5912I Radical -1 2.39511077068 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;17998;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C17999T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:17941-18057&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") orf1ab 17998 T I 5912 orf1ab:T5912I Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;17998;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C17999T", "CodAlignView") B.1.351 Not fixed in B.1.351. 21614 C21614T C T S 21614 L F 18 S:L18F Radical 0 2.87500545351 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21613;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++A++++++++++++++++T+++++++++++++++++++++++++++++++++++'@-57&f=C21614T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21557-21673&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 21614 L F 18 S:L18F Radical 0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21613;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++A++++++++++++++++T+++++++++++++++++++++++++++++++++++'@-57&f=C21614T", "CodAlignView") B.1.351,P.1 Not fixed in B.1.351. Evidence of positive selection in SARS-CoV-2 (Tegally et al). 21621 C21621A C A S 21620 T N 20 S:T20N Radical 0 7.26698076144 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21620;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++T++++++A++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++'@-58&f=C21621A", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21563-21679&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 21620 T N 20 S:T20N Radical 0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21620;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++T++++++A++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++'@-58&f=C21621A", "CodAlignView") P.1 21638 C21638T C T S 21638 P S 26 S:P26S Radical -1 6.47555951381 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21637;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++T++++++A++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C21638T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21581-21697&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 21638 P S 26 S:P26S Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21637;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++T++++++A++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C21638T", "CodAlignView") P.1 21765 21765-21770 deletion S 21767 69 S:del69-70 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21764;6;0&p=52&e=50&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++------++++++++++++++++++++++++++++++C+++++++++++++++++++'@-52&f=21765-21770%20del", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21713-21820&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 21767 69 S:del69-70 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21764;6;0&p=52&e=50&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++------++++++++++++++++++++++++++++++C+++++++++++++++++++'@-52&f=21765-21770%20del", "CodAlignView") B.1.1.7 Deletion in poorly conserved region of S1 that has other deletions. Can cause S dropout in PCR assays. Arose independenly in immune-suppressed individual treated with convalescent plasma (Kemp et al). 21801 A21801C A C S 21800 D A 80 S:D80A Radical -2 1.27316378724 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21800;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++------++++++++++++++++++++++++++++++C++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A21801C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21743-21859&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 21800 D A 80 S:D80A Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21800;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++------++++++++++++++++++++++++++++++C++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A21801C", "CodAlignView") B.1.351 Evidence of positive selection in SARS-CoV-2 (Tegally et al). 21974 G21974T G T S 21974 D Y 138 S:D138Y Radical -3 2.42282740239 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21973;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++---++++++++++++++++++++++++++++++++++++++++'@-57&f=G21974T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21917-22033&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 21974 D Y 138 S:D138Y Radical -3 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21973;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++---++++++++++++++++++++++++++++++++++++++++'@-57&f=G21974T", "CodAlignView") P.1 21991 21991-21993 deletion S 21992 144 S:del144 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21990;3;0&p=53&e=52&w=0&cp=2&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++T++++++++++++++++---++++++++++++++++++++++++++++++++++++++++++++++++++++'@-53&f=21991-21993%20del", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:21938-22045&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 21992 144 S:del144 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;21990;3;0&p=53&e=52&w=0&cp=2&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++T++++++++++++++++---++++++++++++++++++++++++++++++++++++++++++++++++++++'@-53&f=21991-21993%20del", "CodAlignView") B.1.1.7 Deletion in poorly conserved region of S1 that has other deletions. 22132 G22132T G T S 22130 R S 190 S:R190S Radical -1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22131;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G22132T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22073-22189&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 22130 R S 190 S:R190S Radical -1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22131;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G22132T", "CodAlignView") P.1 Conserved amino acid in highly variable section of S1. 22206 A22206G A G S 22205 D G 215 S:D215G Radical -1 1.75753872301 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22205;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A22206G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22148-22264&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 22205 D G 215 S:D215G Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22205;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A22206G", "CodAlignView") B.1.351 Not fixed in B.1.351. Evidence of positive selection in SARS-CoV-2 (Tegally et al). 22286 22286-22294 deletion S 22286 242 S:del242-244 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22285;9;0&p=54&e=45&w=0&cp=0&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++-A-------++++T++++++++++++++++++++++++++++++++++++++++'@-54&f=22286-22294%20del", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22232-22339&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 22286 242 S:del242-244 Deletion =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22285;9;0&p=54&e=45&w=0&cp=0&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++-A-------++++T++++++++++++++++++++++++++++++++++++++++'@-54&f=22286-22294%20del", "CodAlignView") B.1.351 Unresolved and not fixed in B.1.351. 22287 T22287A T A S 22286 L H 242 S:L242H Radical -3 1.52115710575 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22286;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++-A-------++++T++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=T22287A", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22229-22345&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 22286 L H 242 S:L242H Radical -3 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22286;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++-A-------++++T++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=T22287A", "CodAlignView") B.1.351 Unresolved and not fixed in B.1.351. 22299 G22299T G T S 22298 R I 246 S:R246I Radical -3 3.65081908527 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22298;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++-A-------++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=G22299T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22241-22357&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 22298 R I 246 S:R246I Radical -3 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22298;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++-A-------++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=G22299T", "CodAlignView") B.1.351 Not fixed in B.1.351. 22812 A22812C A C S 22811 K T 417 S:K417T Radical -1 0.946449688848 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22811;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++CT+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A22812C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22754-22870&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 22811 K T 417 S:K417T Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22811;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++CT+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=A22812C", "CodAlignView") P.1 In receptor-binding domain. Likely contributes toward immune evasion. In string of 9 amino acids that are perfectly conserved except for a radical amino acid difference between SARS-CoV-2/RaTG13 and the rest of the clade at this exact site, in a larger well-conserved region of the protein. 22813 G22813T G T S 22811 K N 417 S:K417N Radical 0 0.946449688848 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22812;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++CT+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G22813T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22754-22870&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 22811 K N 417 S:K417N Radical 0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;22812;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++CT+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G22813T", "CodAlignView") B.1.351 See notes for A22812C. 23012 G23012A G A S 23012 E K 484 S:E484K Conservative 1 8.81897249867 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23011;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++'@-57&f=G23012A", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:22955-23071&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 23012 E K 484 S:E484K Conservative 1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23011;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++'@-57&f=G23012A", "CodAlignView") B.1.351,P.1,P.2 In receptor-binding domain and receptor-binding motif. Might enhance binding affinity to ACE2 receptor. Might contribute to immune evasion. Evidence of positive selection in SARS-CoV-2 (Tegally et al). Poorly conserved region of protein with several indels. 23063 A23063T A T S 23063 N Y 501 S:N501Y Radical -2 8.01542778673 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23062;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'++++++A++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=A23063T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23006-23122&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 23063 N Y 501 S:N501Y Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23062;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'++++++A++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=A23063T", "CodAlignView") B.1.1.7,B.1.351,P.1 In receptor-binding domain and receptor-binding motif. Enhances binding affinity to ACE2 receptor. Evidence of positive selection in SARS-CoV-2 (Tegally et al). Highly variable amino acid in highly variable region of the protein. 23271 C23271A C A S 23270 A D 570 S:A570D Radical -2 0.972681980835 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23270;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C23271A", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23213-23329&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 23270 A D 570 S:A570D Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23270;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C23271A", "CodAlignView") B.1.1.7 23525 C23525T C T S 23525 H Y 655 S:H655Y Conservative 2 0.428114979145 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23524;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C23525T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23468-23584&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 23525 H Y 655 S:H655Y Conservative 2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23524;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C23525T", "CodAlignView") P.1 23604 C23604A C A S 23603 P H 681 S:P681H Radical -2 6.38518915417 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23603;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C23604A", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23546-23662&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 23603 P H 681 S:P681H Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23603;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++A++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C23604A", "CodAlignView") B.1.1.7 23664 C23664T C T S 23663 A V 701 S:A701V Radical 0 0.855078726813 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23663;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++'@-58&f=C23664T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23606-23722&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 23663 A V 701 S:A701V Radical 0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23663;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++'@-58&f=C23664T", "CodAlignView") B.1.351 23709 C23709T C T S 23708 T I 716 S:T716I Radical -1 0.422821135867 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23708;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++T++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C23709T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:23651-23767&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 23708 T I 716 S:T716I Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;23708;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'+++++++++++++T++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C23709T", "CodAlignView") B.1.1.7 24506 T24506G T G S 24506 S A 982 S:S982A Conservative 1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;24505;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=T24506G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:24449-24565&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 24506 S A 982 S:S982A Conservative 1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;24505;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=T24506G", "CodAlignView") B.1.1.7 Conservative amino acid change in extremely well-conserved region of S2 (43 amino acids with 0 changes). 24642 C24642T C T S 24641 T I 1027 S:T1027I Radical -1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;24641;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C24642T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:24584-24700&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 24641 T I 1027 S:T1027I Radical -1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;24641;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C24642T", "CodAlignView") P.1 Radical change in string of 13 perfectly conserved amino acids in S2. 24914 G24914C G C S 24914 D H 1118 S:D1118H Radical -1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;24913;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G24914C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:24857-24973&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 24914 D H 1118 S:D1118H Radical -1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;24913;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G24914C", "CodAlignView") B.1.1.7 Radical amino acid change in moderately conserved section of S2. 25088 G25088T G T S 25088 V F 1176 S:V1176F Radical -1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25087;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G25088T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25031-25147&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") S 25088 V F 1176 S:V1176F Radical -1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25087;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G25088T", "CodAlignView") P.1,P.2 This section of S2 is well-conserved except in the two most distantly related strains. 25563 G25563T G T ORF3a 25561 Q H 57 ORF3a:Q57H Radical 0 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25562;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=G25563T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25504-25620&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF3c 25562 R I 36 ORF3c:R36I Radical -3 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25562;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=G25563T", "CodAlignView") B.1.351 Radical change in ORF3a and ORF3c. LOF in ORF3d (which is probably not protein-coding). 25904 C25904T C T ORF3a 25903 S L 171 ORF3a:S171L Radical -2 5.50468916329 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25903;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C25904T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:25846-25962&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF3a 25903 S L 171 ORF3a:S171L Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;25903;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C25904T", "CodAlignView") B.1.351 26149 T26149C T C ORF3a 26149 S P 253 ORF3a:S253P Radical -1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26148;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=T26149C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:26092-26208&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF3a 26149 S P 253 ORF3a:S253P Radical -1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26148;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=T26149C", "CodAlignView") P.1 Radical amino acid change in a moderately conserved region near the end of ORF3a that is also synonymously constrained. 26456 C26456T C T E 26455 P L 71 E:P71L Radical -3 4.50853491232 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26455;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C26456T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:26398-26514&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") E 26455 P L 71 E:P71L Radical -3 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26455;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C26456T", "CodAlignView") B.1.351 26645 C26645T C T M 26643 N N 41 M:N41N Synonymous 15.4028504311 1.06424616307e-05 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26644;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C26645T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:26586-26702&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") M 26643 N N 41 M:N41N Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26644;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C26645T", "CodAlignView") B.1.351 Not fixed in B.1.351. 26801 C26801T C T M 26799 L L 93 M:L93L Synonymous 0.806417446641 0.762663947612 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26800;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C26801T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:26742-26858&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") M 26799 L L 93 M:L93L Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;26800;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=C26801T", "CodAlignView") B.1.1.7 Missing from almost all B.1.1.7 genomes. 27504 T27504C T C ORF7a 27502 S S 37 ORF7a:S37S Synonymous 3.25780229911 0.0564310655279 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27503;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=T27504C", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:27445-27561&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF7a 27502 S S 37 ORF7a:S37S Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27503;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C+++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-59&f=T27504C", "CodAlignView") B.1.351 Not fixed in B.1.351. 27972 C27972T C T ORF8 27972 Q * 27 ORF8:Q27* Radical None 1.54347389771 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27971;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C27972T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:27915-28031&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF8 27972 Q * 27 ORF8:Q27* Radical None =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;27971;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=C27972T", "CodAlignView") B.1.1.7 Presumably disables ORF8. A back mutation restoring ORF8 occurred independently in many lineages. 28048 G28048T G T ORF8 28047 R I 52 ORF8:R52I Radical -3 0.311537602708 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28047;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=G28048T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:27990-28106&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF8 28047 R I 52 ORF8:R52I Radical -3 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28047;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=G28048T", "CodAlignView") B.1.1.7 28111 A28111G A G ORF8 28110 Y C 73 ORF8:Y73C Radical -2 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28110;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++A++'@-58&f=A28111G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28053-28169&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF8 28110 Y C 73 ORF8:Y73C Radical -2 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28110;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G+++++++++++++++++++++++++++++++++++++++++++++++++++++++A++'@-58&f=A28111G", "CodAlignView") B.1.1.7 Poorly conserved region of ORF8. 28167 G28167A G A ORF8 28167 E K 92 ORF8:E92K Conservative 1 2.83743819716 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28166;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+G+++++++++++++++++++++++++++++++++++++++++++++++++++++++A+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G28167A", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28110-28226&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF8 28167 E K 92 ORF8:E92K Conservative 1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28166;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+G+++++++++++++++++++++++++++++++++++++++++++++++++++++++A+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G28167A", "CodAlignView") P.1 28253 C28253T C T ORF8 28251 F F 120 ORF8:F120F Synonymous 0.326931131198 0.225358486033 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28252;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++CTA++++++++++++++++++++++++++++'@-59&f=C28253T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28194-28310&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") ORF8 28251 F F 120 ORF8:F120F Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28252;1;0&p=59&e=57&w=0&cp=2&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++CTA++++++++++++++++++++++++++++'@-59&f=C28253T", "CodAlignView") B.1.351,P.2 28280 28280 GAT->CTA GAT CTA N 28280 D L 3 N:D3L Radical -4 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28279;3;0&p=54&e=51&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++T++++++++++++++++++++++++++CTA+++++++++++++++++++++++++++++++++++++++++++++++++++'@-54&f=28280%20GAT-%3ECTA", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28226-28333&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") N 28280 D L 3 N:D3L Radical -4 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28279;3;0&p=54&e=51&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++T++++++++++++++++++++++++++CTA+++++++++++++++++++++++++++++++++++++++++++++++++++'@-54&f=28280%20GAT-%3ECTA", "CodAlignView") B.1.1.7 Changes ORF9b start context from strong to adequate. 28512 C28512G C G N 28511 P R 80 N:P80R Radical -2 15.9336547598 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28511;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C28512G", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28454-28570&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") N 28511 P R 80 N:P80R Radical -2 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28511;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++G++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C28512G", "CodAlignView") P.1 28628 G28628T G T N 28628 A S 119 N:A119S Conservative 1 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28627;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G28628T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28571-28687&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") N 28628 A S 119 N:A119S Conservative 1 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28627;1;0&p=57&e=59&w=0&cp=0&mp=Alt+Alleles:'+++++++++++++++++++++++++++++++++++++++++++++++++++++++++T+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-57&f=G28628T", "CodAlignView") P.2 Conservative amino acid change in string of 16 perfectly-conserved amino acids of N. 28877 28877 AG->TC AG TC N 28877 S S 202 N:S202S Synonymous 0.507877187314 0.473264818519 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28876;2;0&p=54&e=52&w=0&cp=0&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++TC++++++++T+++++++++++++++++++++++++++++++++++++++++++'@-54&f=28877%20AG-%3ETC", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28823-28930&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") N 28877 S S 202 N:S202S Synonymous =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28876;2;0&p=54&e=52&w=0&cp=0&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++TC++++++++T+++++++++++++++++++++++++++++++++++++++++++'@-54&f=28877%20AG-%3ETC", "CodAlignView") P.1 In ORF 9c (which is probably not protein-coding) 28887 C28887T C T N 28886 T I 205 N:T205I Radical -1 8.204194063 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28886;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++TC++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C28887T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28829-28945&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") N 28886 T I 205 N:T205I Radical -1 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28886;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++TC++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C28887T", "CodAlignView") B.1.351 In ORF 9c (which is probably not protein-coding) 28977 C28977T C T N 28976 S F 235 N:S235F Radical -2 Conserved 0.0 =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28976;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C28977T", "CodAlignView") =hyperlink("http://genome.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=NC_045512v2:28919-29035&complement_wuhCor1=0&hgt.revCmplDisp_wuhCor1=0", "UCSCview") N 28976 S F 235 N:S235F Radical -2 Conserved =hyperlink("https://data.broadinstitute.org/compbio1/cav.php?a=wuhCor1_c&i=NC_045512.2;28976;1;0&p=58&e=58&w=0&cp=1&mp=Alt+Alleles:'++++++++++++++++++++++++++++++++++++++++++++++++++++++++++T++++++++++++++++++++++++++++++++++++++++++++++++++++++++++'@-58&f=C28977T", "CodAlignView") B.1.1.7 Conserved amino acid in moderately conserved region of N.