Table 2.

Sequence Harmony results

				Consensus stringd
Region	Amino acid positiona	SH-scoresb	Z-scoresc	High CrNAe	Low CrNAf	Clusterg
C1	E32	0.825	−5.5	Egd	Edkng	1
C1	K33	0.765	−6.7	KQn_e	QNdek	1
C1	V85	0.792	−4.8	Vkaei	Ver	2
C1	V87	0.843	−4.9	Ekg	Eadg	2
C1	K97	0.840	−5.1	Kint	Knr	3
C1	K130	0.843	−8.5	Ne	Nd	4
V1	L134	0.620	−11.4	Lf	VL_aim	5
V1	K135	0.346	−17.0	RKeqg	-hknwg	5
V1	N136	0.698	−12.9	Nt	N-t	5
V1	T138	0.585	−14.4	Tn_	-gast	6
V1	N139	0.650	−12.5	N_t	-nist	6
V1	T140	0.531	−12.0	Tiks_n	-alns	6
V1	.141	0.522	−13.2	T-spgn	SR-egk	6
V1	.141	0.368	−38.3	-tn	N	6
V1	.141	0.223	−24.4	-sktni	TAeiv	6
V1	.141	0.000	−69.1	-h	T	6
V1	.141	0.000	−45.6	-	Nads	6
V1	.141	0.664	−16.1	-ts	Tnsa_	6
V1	N141	0.418	−21.7	NTs	N-tip	6
V1	S142	0.697	−12.1	Ns	Nt_i	6
V1	.145	0.518	−17.3	W-g	Snw_
V1	.146	0.507	−15.8	-m	LI-vg
V1	K151	0.696	−8.3	E-GRtak	GK-qte	6
C2	E268	0.814	−4.6	Ekqg	Edgr	7
C2	V271	0.719	−15.3	Vi	Va	8
C2	V275	0.587	−9.0	Eknvad	Esnqk	3
V3	K322	0.611	−17.4	DE	Eaq	9
C3	I333	0.804	−15.5	Li	Il	10
C3	A336	0.684	−9.1	TAgvel	Aekv	10
C3	K337	0.686	−10.1	EQKntd	Knq	10
C3	K343	0.667	−8.4	Kqsg	EQKgnh	11
C3	A346	0.809	−15.9	AV	V	11
C3	S347	0.837	−3.1	TIndesk	NKEITr	11
V4	F396	0.578	−16.4	NT-wf	-NG	11
V4	T399	0.604	−10.9	-vt	RT-ans	11
V4	.403	0.686	−16.1	-t	N-s
V4	.404	0.537	−11.7	-ksr	KT-epn
V4	S405	0.661	−15.4	-Sdl	-evs	10
V4	N406	0.377	−34.9	N_t	-n	10
V4	N407	0.277	−18.9	N_srk	-thn	10
V4	.412	0.574	−13.5	-s	N-wde
V4	.412	0.689	−11.6	-	-snt
C4	S440	0.729	−6.8	Raks	KReg	12
V5	S461	0.650	−14.0	DE-sn	-n
V5	.464	0.692	−9.4	NEK-	-rk	13
V5	.464	0.557	−15.2	-nda	-Nti	13
gp41	Q621	0.540	−9.4	Kestardq	EMYQNK

^aAmino acid numbering based on the HXB2 reference sequence.

^bSequence Harmony scores (SH-scores): SH-scores below a cut-off of <0.7 for variable regions and a cut-off of <0.85 for conserved regions are shown.

^cThe z-scores display the accuracy of a given result; the more negative the z-score the less likely it is that the results was found by chance.

^dThe ’consensus string’ shows the residues found in each group on that specific site ordered by frequency were a lower case letter is present less than half the amount of the most abundant residue (upper case).

^eIndividuals who developed CrNA.

^fIndividuals who did not develop CrNA.

^gNumbers represent the subclusters as defined in Additional file 5: Table S2.