Gene_Name	AA_alt	sample	DP	AD_alt	AF	lineage
M	I82T	SampleC_freebayes_ann	3984	2770	0.695281124497992	AY.1
N	D63G	SampleC_freebayes_ann	2180	787	0.361009174311927	AY.1
N	R203M	SampleC_freebayes_ann	4147	4125	0.994694960212202	AY.1
N	G215C	SampleC_freebayes_ann	4477	2574	0.574938574938575	AY.1
N	D377Y	SampleC_freebayes_ann	4271	1623	0.380004682744088	AY.1
ORF1a	A1306S	SampleC_freebayes_ann	2202	1267	0.575386012715713	AY.1
ORF1a	P2046L	SampleC_freebayes_ann	2996	1763	0.58845126835781	AY.1
ORF1a	P2287S	SampleC_freebayes_ann	2633	1563	0.59361944549943	AY.1
ORF1a	V2930L	SampleC_freebayes_ann	1082	913	0.843807763401109	AY.1
ORF1a	T3255I	SampleC_freebayes_ann	857	437	0.509918319719953	AY.1
ORF1a	T3646A	SampleC_freebayes_ann	801	744	0.928838951310862	AY.1
ORF3a	S26L	SampleC_freebayes_ann	4510	3826	0.848337028824834	AY.1
ORF7a	V82A	SampleC_freebayes_ann	4141	2302	0.555904370924897	AY.1
ORF7a	T120I	SampleC_freebayes_ann	4981	2730	0.548082714314395	AY.1
S	T19R	SampleC_freebayes_ann	2058	1448	0.703595724003887	AY.1
S	L452R	SampleC_freebayes_ann	1753	1147	0.654306902452938	AY.1
S	T478K	SampleC_freebayes_ann	1708	1088	0.637002341920375	AY.1
S	D614G	SampleA_freebayes_ann	41	41	1	AY.1
S	D614G	SampleB_freebayes_ann	15	15	1	AY.1
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	AY.1
S	P681R	SampleC_freebayes_ann	536	536	1	AY.1
S	D950N	SampleC_freebayes_ann	949	368	0.387776606954689	AY.1
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	AY.1
ORF1b	G662S	SampleA_freebayes_ann	0	0	0	AY.1
ORF1b	P1000L	SampleB_freebayes_ann	0	0	0	AY.1
ORF1b	A1918V	SampleC_freebayes_ann	0	0	0	AY.1
ORF7b	T40I	SampleA_freebayes_ann	0	0	0	AY.1
ORF8	D119I	SampleB_freebayes_ann	0	0	0	AY.1
ORF8	del120/121	SampleC_freebayes_ann	0	0	0	AY.1
S	E156G	SampleA_freebayes_ann	0	0	0	AY.1
S	del157/158	SampleB_freebayes_ann	0	0	0	AY.1
S	W258L	SampleC_freebayes_ann	0	0	0	AY.1
S	K417N	SampleA_freebayes_ann	0	0	0	AY.1
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	AY.1
ORF1b	G662S	SampleC_freebayes_ann	0	0	0	AY.1
ORF1b	P1000L	SampleA_freebayes_ann	0	0	0	AY.1
ORF1b	A1918V	SampleB_freebayes_ann	0	0	0	AY.1
ORF7b	T40I	SampleC_freebayes_ann	0	0	0	AY.1
ORF8	D119I	SampleA_freebayes_ann	0	0	0	AY.1
ORF8	del120/121	SampleB_freebayes_ann	0	0	0	AY.1
S	E156G	SampleC_freebayes_ann	0	0	0	AY.1
S	del157/158	SampleA_freebayes_ann	0	0	0	AY.1
S	W258L	SampleB_freebayes_ann	0	0	0	AY.1
S	K417N	SampleC_freebayes_ann	0	0	0	AY.1
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	AY.1
ORF1b	G662S	SampleB_freebayes_ann	0	0	0	AY.1
ORF1b	P1000L	SampleC_freebayes_ann	0	0	0	AY.1
ORF1b	A1918V	SampleA_freebayes_ann	0	0	0	AY.1
ORF7b	T40I	SampleB_freebayes_ann	0	0	0	AY.1
ORF8	D119I	SampleC_freebayes_ann	0	0	0	AY.1
ORF8	del120/121	SampleA_freebayes_ann	0	0	0	AY.1
S	E156G	SampleB_freebayes_ann	0	0	0	AY.1
S	del157/158	SampleC_freebayes_ann	0	0	0	AY.1
S	W258L	SampleA_freebayes_ann	0	0	0	AY.1
S	K417N	SampleB_freebayes_ann	0	0	0	AY.1
M	I82T	SampleC_freebayes_ann	3984	2770	0.695281124497992	AY.2
N	D63G	SampleC_freebayes_ann	2180	787	0.361009174311927	AY.2
N	R203M	SampleC_freebayes_ann	4147	4125	0.994694960212202	AY.2
N	D377Y	SampleC_freebayes_ann	4271	1623	0.380004682744088	AY.2
ORF1a	P1640L	SampleC_freebayes_ann	1997	332	0.166249374061092	AY.2
ORF1a	A3209V	SampleC_freebayes_ann	1065	373	0.350234741784038	AY.2
ORF1a	V3718A	SampleC_freebayes_ann	2727	444	0.162816281628163	AY.2
ORF1a	T3750I	SampleC_freebayes_ann	2189	349	0.159433531292828	AY.2
ORF3a	S26L	SampleC_freebayes_ann	4510	3826	0.848337028824834	AY.2
ORF7a	V82A	SampleC_freebayes_ann	4141	2302	0.555904370924897	AY.2
ORF7a	T120I	SampleC_freebayes_ann	4981	2730	0.548082714314395	AY.2
S	T19R	SampleC_freebayes_ann	2058	1448	0.703595724003887	AY.2
S	L452R	SampleC_freebayes_ann	1753	1147	0.654306902452938	AY.2
S	T478K	SampleC_freebayes_ann	1708	1088	0.637002341920375	AY.2
S	D614G	SampleA_freebayes_ann	41	41	1	AY.2
S	D614G	SampleB_freebayes_ann	15	15	1	AY.2
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	AY.2
S	P681R	SampleC_freebayes_ann	536	536	1	AY.2
S	D950N	SampleC_freebayes_ann	949	368	0.387776606954689	AY.2
ORF1a	A1146T	SampleC_freebayes_ann	0	0	0	AY.2
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	AY.2
ORF1b	G662S	SampleB_freebayes_ann	0	0	0	AY.2
ORF1b	P1000L	SampleC_freebayes_ann	0	0	0	AY.2
ORF1b	T1290I	SampleA_freebayes_ann	0	0	0	AY.2
ORF8	D119I	SampleB_freebayes_ann	0	0	0	AY.2
ORF8	del120/121	SampleC_freebayes_ann	0	0	0	AY.2
S	V70F	SampleA_freebayes_ann	0	0	0	AY.2
S	E156G	SampleB_freebayes_ann	0	0	0	AY.2
S	del157/158	SampleC_freebayes_ann	0	0	0	AY.2
S	A222V	SampleA_freebayes_ann	0	0	0	AY.2
S	K417N	SampleB_freebayes_ann	0	0	0	AY.2
ORF1a	A1146T	SampleC_freebayes_ann	0	0	0	AY.2
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	AY.2
ORF1b	G662S	SampleB_freebayes_ann	0	0	0	AY.2
ORF1b	P1000L	SampleC_freebayes_ann	0	0	0	AY.2
ORF1b	T1290I	SampleA_freebayes_ann	0	0	0	AY.2
ORF8	D119I	SampleB_freebayes_ann	0	0	0	AY.2
ORF8	del120/121	SampleC_freebayes_ann	0	0	0	AY.2
S	V70F	SampleA_freebayes_ann	0	0	0	AY.2
S	E156G	SampleB_freebayes_ann	0	0	0	AY.2
S	del157/158	SampleC_freebayes_ann	0	0	0	AY.2
S	A222V	SampleA_freebayes_ann	0	0	0	AY.2
S	K417N	SampleB_freebayes_ann	0	0	0	AY.2
ORF1a	A1146T	SampleC_freebayes_ann	0	0	0	AY.2
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	AY.2
ORF1b	G662S	SampleB_freebayes_ann	0	0	0	AY.2
ORF1b	P1000L	SampleC_freebayes_ann	0	0	0	AY.2
ORF1b	T1290I	SampleA_freebayes_ann	0	0	0	AY.2
ORF8	D119I	SampleB_freebayes_ann	0	0	0	AY.2
ORF8	del120/121	SampleC_freebayes_ann	0	0	0	AY.2
S	V70F	SampleA_freebayes_ann	0	0	0	AY.2
S	E156G	SampleB_freebayes_ann	0	0	0	AY.2
S	del157/158	SampleC_freebayes_ann	0	0	0	AY.2
S	A222V	SampleA_freebayes_ann	0	0	0	AY.2
S	K417N	SampleB_freebayes_ann	0	0	0	AY.2
M	I82T	SampleC_freebayes_ann	3984	2770	0.695281124497992	AY.3.1
N	D63G	SampleC_freebayes_ann	2180	787	0.361009174311927	AY.3.1
N	R203M	SampleC_freebayes_ann	4147	4125	0.994694960212202	AY.3.1
N	G215C	SampleC_freebayes_ann	4477	2574	0.574938574938575	AY.3.1
N	D377Y	SampleC_freebayes_ann	4271	1623	0.380004682744088	AY.3.1
ORF1a	A1306S	SampleC_freebayes_ann	2202	1267	0.575386012715713	AY.3.1
ORF1a	P2046L	SampleC_freebayes_ann	2996	1763	0.58845126835781	AY.3.1
ORF1a	P2287S	SampleC_freebayes_ann	2633	1563	0.59361944549943	AY.3.1
ORF1a	V2930L	SampleC_freebayes_ann	1082	913	0.843807763401109	AY.3.1
ORF1a	T3255I	SampleC_freebayes_ann	857	437	0.509918319719953	AY.3.1
ORF1a	T3646A	SampleC_freebayes_ann	801	744	0.928838951310862	AY.3.1
ORF1b	H5944Y	SampleB_freebayes_ann	96	1	0.0104166666666667	AY.3.1
ORF3a	S26L	SampleC_freebayes_ann	4510	3826	0.848337028824834	AY.3.1
ORF7a	V82A	SampleC_freebayes_ann	4141	2302	0.555904370924897	AY.3.1
ORF7a	T120I	SampleC_freebayes_ann	4981	2730	0.548082714314395	AY.3.1
S	T19R	SampleC_freebayes_ann	2058	1448	0.703595724003887	AY.3.1
S	L452R	SampleC_freebayes_ann	1753	1147	0.654306902452938	AY.3.1
S	T478K	SampleC_freebayes_ann	1708	1088	0.637002341920375	AY.3.1
S	D614G	SampleA_freebayes_ann	41	41	1	AY.3.1
S	D614G	SampleB_freebayes_ann	15	15	1	AY.3.1
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	AY.3.1
S	P681R	SampleC_freebayes_ann	536	536	1	AY.3.1
S	D950N	SampleC_freebayes_ann	949	368	0.387776606954689	AY.3.1
ORF1a	D1127Y	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF1a	I3731V	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF1b	G662S	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF1b	P1000L	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF1b	A1918V	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF7b	T40I	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF8	D119I	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF8	del120/121	SampleA_freebayes_ann	0	0	0	AY.3.1
S	E156G	SampleC_freebayes_ann	0	0	0	AY.3.1
S	del157/158	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF1a	D1127Y	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF1a	I3731V	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF1b	G662S	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF1b	P1000L	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF1b	A1918V	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF7b	T40I	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF8	D119I	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF8	del120/121	SampleB_freebayes_ann	0	0	0	AY.3.1
S	E156G	SampleA_freebayes_ann	0	0	0	AY.3.1
S	del157/158	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF1a	D1127Y	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF1a	I3731V	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF1b	G662S	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF1b	P1000L	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF1b	A1918V	SampleC_freebayes_ann	0	0	0	AY.3.1
ORF7b	T40I	SampleB_freebayes_ann	0	0	0	AY.3.1
ORF8	D119I	SampleA_freebayes_ann	0	0	0	AY.3.1
ORF8	del120/121	SampleC_freebayes_ann	0	0	0	AY.3.1
S	E156G	SampleB_freebayes_ann	0	0	0	AY.3.1
S	del157/158	SampleA_freebayes_ann	0	0	0	AY.3.1
M	I82T	SampleC_freebayes_ann	3984	2770	0.695281124497992	AY.3
N	D63G	SampleC_freebayes_ann	2180	787	0.361009174311927	AY.3
N	R203M	SampleC_freebayes_ann	4147	4125	0.994694960212202	AY.3
N	G215C	SampleC_freebayes_ann	4477	2574	0.574938574938575	AY.3
N	D377Y	SampleC_freebayes_ann	4271	1623	0.380004682744088	AY.3
ORF1a	A1306S	SampleC_freebayes_ann	2202	1267	0.575386012715713	AY.3
ORF1a	P2046L	SampleC_freebayes_ann	2996	1763	0.58845126835781	AY.3
ORF1a	P2287S	SampleC_freebayes_ann	2633	1563	0.59361944549943	AY.3
ORF1a	V2930L	SampleC_freebayes_ann	1082	913	0.843807763401109	AY.3
ORF1a	T3255I	SampleC_freebayes_ann	857	437	0.509918319719953	AY.3
ORF1a	T3646A	SampleC_freebayes_ann	801	744	0.928838951310862	AY.3
ORF3a	S26L	SampleC_freebayes_ann	4510	3826	0.848337028824834	AY.3
ORF7a	V82A	SampleC_freebayes_ann	4141	2302	0.555904370924897	AY.3
ORF7a	T120I	SampleC_freebayes_ann	4981	2730	0.548082714314395	AY.3
S	T19R	SampleC_freebayes_ann	2058	1448	0.703595724003887	AY.3
S	L452R	SampleC_freebayes_ann	1753	1147	0.654306902452938	AY.3
S	T478K	SampleC_freebayes_ann	1708	1088	0.637002341920375	AY.3
S	D614G	SampleA_freebayes_ann	41	41	1	AY.3
S	D614G	SampleB_freebayes_ann	15	15	1	AY.3
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	AY.3
S	P681R	SampleC_freebayes_ann	536	536	1	AY.3
S	D950N	SampleC_freebayes_ann	949	368	0.387776606954689	AY.3
ORF1a	I3731V	SampleC_freebayes_ann	0	0	0	AY.3
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	AY.3
ORF1b	G662S	SampleB_freebayes_ann	0	0	0	AY.3
ORF1b	P1000L	SampleC_freebayes_ann	0	0	0	AY.3
ORF1b	A1918V	SampleA_freebayes_ann	0	0	0	AY.3
ORF7b	T40I	SampleB_freebayes_ann	0	0	0	AY.3
ORF8	D119I	SampleC_freebayes_ann	0	0	0	AY.3
ORF8	del120/121	SampleA_freebayes_ann	0	0	0	AY.3
S	E156G	SampleB_freebayes_ann	0	0	0	AY.3
S	del157/158	SampleC_freebayes_ann	0	0	0	AY.3
ORF1a	I3731V	SampleA_freebayes_ann	0	0	0	AY.3
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	AY.3
ORF1b	G662S	SampleC_freebayes_ann	0	0	0	AY.3
ORF1b	P1000L	SampleA_freebayes_ann	0	0	0	AY.3
ORF1b	A1918V	SampleB_freebayes_ann	0	0	0	AY.3
ORF7b	T40I	SampleC_freebayes_ann	0	0	0	AY.3
ORF8	D119I	SampleA_freebayes_ann	0	0	0	AY.3
ORF8	del120/121	SampleB_freebayes_ann	0	0	0	AY.3
S	E156G	SampleC_freebayes_ann	0	0	0	AY.3
S	del157/158	SampleA_freebayes_ann	0	0	0	AY.3
ORF1a	I3731V	SampleB_freebayes_ann	0	0	0	AY.3
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	AY.3
ORF1b	G662S	SampleA_freebayes_ann	0	0	0	AY.3
ORF1b	P1000L	SampleB_freebayes_ann	0	0	0	AY.3
ORF1b	A1918V	SampleC_freebayes_ann	0	0	0	AY.3
ORF7b	T40I	SampleA_freebayes_ann	0	0	0	AY.3
ORF8	D119I	SampleB_freebayes_ann	0	0	0	AY.3
ORF8	del120/121	SampleC_freebayes_ann	0	0	0	AY.3
S	E156G	SampleA_freebayes_ann	0	0	0	AY.3
S	del157/158	SampleB_freebayes_ann	0	0	0	AY.3
N	D3L	SampleA_freebayes_ann	54	54	1	B.1.1.7
N	D3L	SampleB_freebayes_ann	200	200	1	B.1.1.7
N	D3L	SampleC_freebayes_ann	6314	3423	0.542128603104213	B.1.1.7
N	RG203KR	SampleA_freebayes_ann	14	14	1	B.1.1.7
N	RG203KR	SampleB_freebayes_ann	69	68	0.985507246376812	B.1.1.7
N	S235F	SampleA_freebayes_ann	14	14	1	B.1.1.7
N	S235F	SampleB_freebayes_ann	65	61	0.938461538461539	B.1.1.7
N	S235F	SampleC_freebayes_ann	3909	1501	0.383985674085444	B.1.1.7
ORF1a	T1001I	SampleA_freebayes_ann	35	35	1	B.1.1.7
ORF1a	T1001I	SampleB_freebayes_ann	51	51	1	B.1.1.7
ORF1a	T1001I	SampleC_freebayes_ann	3354	2829	0.843470483005367	B.1.1.7
ORF1a	A1708D	SampleA_freebayes_ann	44	32	0.727272727272727	B.1.1.7
ORF1a	A1708D	SampleB_freebayes_ann	69	69	1	B.1.1.7
ORF1a	A1708D	SampleC_freebayes_ann	1638	691	0.421855921855922	B.1.1.7
ORF1a	I2230T	SampleC_freebayes_ann	4348	3244	0.746090156393744	B.1.1.7
ORF8	Q27*	SampleA_freebayes_ann	66	66	1	B.1.1.7
ORF8	Q27*	SampleB_freebayes_ann	114	114	1	B.1.1.7
ORF8	Q27*	SampleC_freebayes_ann	1308	150	0.114678899082569	B.1.1.7
ORF8	R52I	SampleA_freebayes_ann	66	66	1	B.1.1.7
ORF8	R52I	SampleB_freebayes_ann	114	114	1	B.1.1.7
ORF8	R52I	SampleC_freebayes_ann	1234	133	0.107779578606159	B.1.1.7
ORF8	Y73C	SampleA_freebayes_ann	59	59	1	B.1.1.7
ORF8	Y73C	SampleB_freebayes_ann	155	155	1	B.1.1.7
ORF8	Y73C	SampleC_freebayes_ann	2841	1482	0.521647307286167	B.1.1.7
S	del69/70	SampleB_freebayes_ann	2	2	1	B.1.1.7
S	del69/70	SampleC_freebayes_ann	744	744	1	B.1.1.7
S	N501Y	SampleA_freebayes_ann	6	6	1	B.1.1.7
S	N501Y	SampleB_freebayes_ann	4	4	1	B.1.1.7
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	B.1.1.7
S	A570D	SampleA_freebayes_ann	42	42	1	B.1.1.7
S	A570D	SampleB_freebayes_ann	16	16	1	B.1.1.7
S	A570D	SampleC_freebayes_ann	3990	99	0.024812030075188	B.1.1.7
S	D614G	SampleA_freebayes_ann	41	41	1	B.1.1.7
S	D614G	SampleB_freebayes_ann	15	15	1	B.1.1.7
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	B.1.1.7
S	P681H	SampleA_freebayes_ann	36	13	0.361111111111111	B.1.1.7
S	P681H	SampleB_freebayes_ann	8	8	1	B.1.1.7
S	T716I	SampleA_freebayes_ann	36	13	0.361111111111111	B.1.1.7
S	T716I	SampleB_freebayes_ann	8	8	1	B.1.1.7
S	S982A	SampleA_freebayes_ann	26	26	1	B.1.1.7
S	S982A	SampleB_freebayes_ann	62	62	1	B.1.1.7
S	S982A	SampleC_freebayes_ann	2224	704	0.316546762589928	B.1.1.7
S	D1118H	SampleA_freebayes_ann	40	40	1	B.1.1.7
S	D1118H	SampleB_freebayes_ann	134	133	0.992537313432836	B.1.1.7
S	D1118H	SampleC_freebayes_ann	4900	1158	0.236326530612245	B.1.1.7
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	B.1.1.7
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	B.1.1.7
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	B.1.1.7
S	del144/145	SampleA_freebayes_ann	0	0	0	B.1.1.7
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	B.1.1.7
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	B.1.1.7
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	B.1.1.7
S	del144/145	SampleB_freebayes_ann	0	0	0	B.1.1.7
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	B.1.1.7
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	B.1.1.7
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	B.1.1.7
S	del144/145	SampleC_freebayes_ann	0	0	0	B.1.1.7
N	D3L	SampleA_freebayes_ann	54	54	1	B.1.1.7+S_E484K
N	D3L	SampleB_freebayes_ann	200	200	1	B.1.1.7+S_E484K
N	D3L	SampleC_freebayes_ann	6314	3423	0.542128603104213	B.1.1.7+S_E484K
N	RG203KR	SampleA_freebayes_ann	14	14	1	B.1.1.7+S_E484K
N	RG203KR	SampleB_freebayes_ann	69	68	0.985507246376812	B.1.1.7+S_E484K
N	S235F	SampleA_freebayes_ann	14	14	1	B.1.1.7+S_E484K
N	S235F	SampleB_freebayes_ann	65	61	0.938461538461539	B.1.1.7+S_E484K
N	S235F	SampleC_freebayes_ann	3909	1501	0.383985674085444	B.1.1.7+S_E484K
ORF1a	T1001I	SampleA_freebayes_ann	35	35	1	B.1.1.7+S_E484K
ORF1a	T1001I	SampleB_freebayes_ann	51	51	1	B.1.1.7+S_E484K
ORF1a	T1001I	SampleC_freebayes_ann	3354	2829	0.843470483005367	B.1.1.7+S_E484K
ORF1a	A1708D	SampleA_freebayes_ann	44	32	0.727272727272727	B.1.1.7+S_E484K
ORF1a	A1708D	SampleB_freebayes_ann	69	69	1	B.1.1.7+S_E484K
ORF1a	A1708D	SampleC_freebayes_ann	1638	691	0.421855921855922	B.1.1.7+S_E484K
ORF1a	I2230T	SampleC_freebayes_ann	4348	3244	0.746090156393744	B.1.1.7+S_E484K
ORF8	Q27*	SampleA_freebayes_ann	66	66	1	B.1.1.7+S_E484K
ORF8	Q27*	SampleB_freebayes_ann	114	114	1	B.1.1.7+S_E484K
ORF8	Q27*	SampleC_freebayes_ann	1308	150	0.114678899082569	B.1.1.7+S_E484K
ORF8	R52I	SampleA_freebayes_ann	66	66	1	B.1.1.7+S_E484K
ORF8	R52I	SampleB_freebayes_ann	114	114	1	B.1.1.7+S_E484K
ORF8	R52I	SampleC_freebayes_ann	1234	133	0.107779578606159	B.1.1.7+S_E484K
ORF8	Y73C	SampleA_freebayes_ann	59	59	1	B.1.1.7+S_E484K
ORF8	Y73C	SampleB_freebayes_ann	155	155	1	B.1.1.7+S_E484K
ORF8	Y73C	SampleC_freebayes_ann	2841	1482	0.521647307286167	B.1.1.7+S_E484K
S	del69/70	SampleB_freebayes_ann	2	2	1	B.1.1.7+S_E484K
S	del69/70	SampleC_freebayes_ann	744	744	1	B.1.1.7+S_E484K
S	N501Y	SampleA_freebayes_ann	6	6	1	B.1.1.7+S_E484K
S	N501Y	SampleB_freebayes_ann	4	4	1	B.1.1.7+S_E484K
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	B.1.1.7+S_E484K
S	A570D	SampleA_freebayes_ann	42	42	1	B.1.1.7+S_E484K
S	A570D	SampleB_freebayes_ann	16	16	1	B.1.1.7+S_E484K
S	A570D	SampleC_freebayes_ann	3990	99	0.024812030075188	B.1.1.7+S_E484K
S	D614G	SampleA_freebayes_ann	41	41	1	B.1.1.7+S_E484K
S	D614G	SampleB_freebayes_ann	15	15	1	B.1.1.7+S_E484K
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	B.1.1.7+S_E484K
S	P681H	SampleA_freebayes_ann	36	13	0.361111111111111	B.1.1.7+S_E484K
S	P681H	SampleB_freebayes_ann	8	8	1	B.1.1.7+S_E484K
S	T716I	SampleA_freebayes_ann	36	13	0.361111111111111	B.1.1.7+S_E484K
S	T716I	SampleB_freebayes_ann	8	8	1	B.1.1.7+S_E484K
S	S982A	SampleA_freebayes_ann	26	26	1	B.1.1.7+S_E484K
S	S982A	SampleB_freebayes_ann	62	62	1	B.1.1.7+S_E484K
S	S982A	SampleC_freebayes_ann	2224	704	0.316546762589928	B.1.1.7+S_E484K
S	D1118H	SampleA_freebayes_ann	40	40	1	B.1.1.7+S_E484K
S	D1118H	SampleB_freebayes_ann	134	133	0.992537313432836	B.1.1.7+S_E484K
S	D1118H	SampleC_freebayes_ann	4900	1158	0.236326530612245	B.1.1.7+S_E484K
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	B.1.1.7+S_E484K
S	del144/145	SampleA_freebayes_ann	0	0	0	B.1.1.7+S_E484K
S	E484K	SampleB_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	B.1.1.7+S_E484K
S	del144/145	SampleC_freebayes_ann	0	0	0	B.1.1.7+S_E484K
S	E484K	SampleA_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	B.1.1.7+S_E484K
S	del144/145	SampleB_freebayes_ann	0	0	0	B.1.1.7+S_E484K
S	E484K	SampleC_freebayes_ann	0	0	0	B.1.1.7+S_E484K
ORF3a	S171L	SampleA_freebayes_ann	11	1	0.0909090909090909	B.1.351.2
S	D80A	SampleA_freebayes_ann	31	11	0.354838709677419	B.1.351.2
S	N501Y	SampleA_freebayes_ann	6	6	1	B.1.351.2
S	N501Y	SampleB_freebayes_ann	4	4	1	B.1.351.2
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	B.1.351.2
S	D614G	SampleA_freebayes_ann	41	41	1	B.1.351.2
S	D614G	SampleB_freebayes_ann	15	15	1	B.1.351.2
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	B.1.351.2
S	A701V	SampleA_freebayes_ann	36	23	0.638888888888889	B.1.351.2
E	P71L	SampleA_freebayes_ann	0	0	0	B.1.351.2
N	T205I	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1a	T265I	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	K1655N	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1a	N2596S	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1a	K3353R	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	A3456V	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF3a	Q57H	SampleB_freebayes_ann	0	0	0	B.1.351.2
S	L18F	SampleC_freebayes_ann	0	0	0	B.1.351.2
S	D215G	SampleA_freebayes_ann	0	0	0	B.1.351.2
S	del241/243	SampleB_freebayes_ann	0	0	0	B.1.351.2
S	K417N	SampleC_freebayes_ann	0	0	0	B.1.351.2
S	E484K	SampleA_freebayes_ann	0	0	0	B.1.351.2
E	P71L	SampleB_freebayes_ann	0	0	0	B.1.351.2
N	T205I	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	T265I	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1a	K1655N	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1a	N2596S	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	K3353R	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1a	A3456V	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF3a	Q57H	SampleC_freebayes_ann	0	0	0	B.1.351.2
S	L18F	SampleA_freebayes_ann	0	0	0	B.1.351.2
S	D215G	SampleB_freebayes_ann	0	0	0	B.1.351.2
S	del241/243	SampleC_freebayes_ann	0	0	0	B.1.351.2
S	K417N	SampleA_freebayes_ann	0	0	0	B.1.351.2
S	E484K	SampleB_freebayes_ann	0	0	0	B.1.351.2
E	P71L	SampleC_freebayes_ann	0	0	0	B.1.351.2
N	T205I	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1a	T265I	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1a	K1655N	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	N2596S	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1a	K3353R	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1a	A3456V	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	B.1.351.2
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	B.1.351.2
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF3a	Q57H	SampleA_freebayes_ann	0	0	0	B.1.351.2
S	L18F	SampleB_freebayes_ann	0	0	0	B.1.351.2
S	D215G	SampleC_freebayes_ann	0	0	0	B.1.351.2
S	del241/243	SampleA_freebayes_ann	0	0	0	B.1.351.2
S	K417N	SampleB_freebayes_ann	0	0	0	B.1.351.2
S	E484K	SampleC_freebayes_ann	0	0	0	B.1.351.2
ORF1a	P2046L	SampleC_freebayes_ann	2996	1763	0.58845126835781	B.1.351.3
ORF3a	S171L	SampleA_freebayes_ann	11	1	0.0909090909090909	B.1.351.3
S	D80A	SampleA_freebayes_ann	31	11	0.354838709677419	B.1.351.3
S	N501Y	SampleA_freebayes_ann	6	6	1	B.1.351.3
S	N501Y	SampleB_freebayes_ann	4	4	1	B.1.351.3
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	B.1.351.3
S	D614G	SampleA_freebayes_ann	41	41	1	B.1.351.3
S	D614G	SampleB_freebayes_ann	15	15	1	B.1.351.3
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	B.1.351.3
S	A701V	SampleA_freebayes_ann	36	23	0.638888888888889	B.1.351.3
E	P71L	SampleC_freebayes_ann	0	0	0	B.1.351.3
N	T205I	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1a	T265I	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1a	K1655N	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1a	N2596S	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1a	K3353R	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1b	I1074V	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF3a	Q57H	SampleA_freebayes_ann	0	0	0	B.1.351.3
S	L18F	SampleB_freebayes_ann	0	0	0	B.1.351.3
S	D215G	SampleC_freebayes_ann	0	0	0	B.1.351.3
S	del241/243	SampleA_freebayes_ann	0	0	0	B.1.351.3
S	K417N	SampleB_freebayes_ann	0	0	0	B.1.351.3
S	E484K	SampleC_freebayes_ann	0	0	0	B.1.351.3
E	P71L	SampleA_freebayes_ann	0	0	0	B.1.351.3
N	T205I	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1a	T265I	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1a	K1655N	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1a	N2596S	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1a	K3353R	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1b	I1074V	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF3a	Q57H	SampleB_freebayes_ann	0	0	0	B.1.351.3
S	L18F	SampleC_freebayes_ann	0	0	0	B.1.351.3
S	D215G	SampleA_freebayes_ann	0	0	0	B.1.351.3
S	del241/243	SampleB_freebayes_ann	0	0	0	B.1.351.3
S	K417N	SampleC_freebayes_ann	0	0	0	B.1.351.3
S	E484K	SampleA_freebayes_ann	0	0	0	B.1.351.3
E	P71L	SampleB_freebayes_ann	0	0	0	B.1.351.3
N	T205I	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1a	T265I	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1a	K1655N	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1a	N2596S	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1a	K3353R	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	B.1.351.3
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	B.1.351.3
ORF1b	I1074V	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF3a	Q57H	SampleC_freebayes_ann	0	0	0	B.1.351.3
S	L18F	SampleA_freebayes_ann	0	0	0	B.1.351.3
S	D215G	SampleB_freebayes_ann	0	0	0	B.1.351.3
S	del241/243	SampleC_freebayes_ann	0	0	0	B.1.351.3
S	K417N	SampleA_freebayes_ann	0	0	0	B.1.351.3
S	E484K	SampleB_freebayes_ann	0	0	0	B.1.351.3
ORF3a	S171L	SampleA_freebayes_ann	11	1	0.0909090909090909	B.1.351
S	D80A	SampleA_freebayes_ann	31	11	0.354838709677419	B.1.351
S	N501Y	SampleA_freebayes_ann	6	6	1	B.1.351
S	N501Y	SampleB_freebayes_ann	4	4	1	B.1.351
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	B.1.351
S	D614G	SampleA_freebayes_ann	41	41	1	B.1.351
S	D614G	SampleB_freebayes_ann	15	15	1	B.1.351
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	B.1.351
S	A701V	SampleA_freebayes_ann	36	23	0.638888888888889	B.1.351
E	P71L	SampleA_freebayes_ann	0	0	0	B.1.351
N	T205I	SampleB_freebayes_ann	0	0	0	B.1.351
ORF1a	T265I	SampleC_freebayes_ann	0	0	0	B.1.351
ORF1a	K1655N	SampleA_freebayes_ann	0	0	0	B.1.351
ORF1a	K3353R	SampleB_freebayes_ann	0	0	0	B.1.351
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	B.1.351
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	B.1.351
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	B.1.351
ORF3a	Q57H	SampleC_freebayes_ann	0	0	0	B.1.351
S	D215G	SampleA_freebayes_ann	0	0	0	B.1.351
S	del241/243	SampleB_freebayes_ann	0	0	0	B.1.351
S	K417N	SampleC_freebayes_ann	0	0	0	B.1.351
S	E484K	SampleA_freebayes_ann	0	0	0	B.1.351
E	P71L	SampleB_freebayes_ann	0	0	0	B.1.351
N	T205I	SampleC_freebayes_ann	0	0	0	B.1.351
ORF1a	T265I	SampleA_freebayes_ann	0	0	0	B.1.351
ORF1a	K1655N	SampleB_freebayes_ann	0	0	0	B.1.351
ORF1a	K3353R	SampleC_freebayes_ann	0	0	0	B.1.351
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	B.1.351
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	B.1.351
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	B.1.351
ORF3a	Q57H	SampleA_freebayes_ann	0	0	0	B.1.351
S	D215G	SampleB_freebayes_ann	0	0	0	B.1.351
S	del241/243	SampleC_freebayes_ann	0	0	0	B.1.351
S	K417N	SampleA_freebayes_ann	0	0	0	B.1.351
S	E484K	SampleB_freebayes_ann	0	0	0	B.1.351
E	P71L	SampleC_freebayes_ann	0	0	0	B.1.351
N	T205I	SampleA_freebayes_ann	0	0	0	B.1.351
ORF1a	T265I	SampleB_freebayes_ann	0	0	0	B.1.351
ORF1a	K1655N	SampleC_freebayes_ann	0	0	0	B.1.351
ORF1a	K3353R	SampleA_freebayes_ann	0	0	0	B.1.351
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	B.1.351
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	B.1.351
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	B.1.351
ORF3a	Q57H	SampleB_freebayes_ann	0	0	0	B.1.351
S	D215G	SampleC_freebayes_ann	0	0	0	B.1.351
S	del241/243	SampleA_freebayes_ann	0	0	0	B.1.351
S	K417N	SampleB_freebayes_ann	0	0	0	B.1.351
S	E484K	SampleC_freebayes_ann	0	0	0	B.1.351
M	I82T	SampleC_freebayes_ann	3984	2770	0.695281124497992	B.1.617.2
N	D63G	SampleC_freebayes_ann	2180	787	0.361009174311927	B.1.617.2
N	R203M	SampleC_freebayes_ann	4147	4125	0.994694960212202	B.1.617.2
N	D377Y	SampleC_freebayes_ann	4271	1623	0.380004682744088	B.1.617.2
ORF3a	S26L	SampleC_freebayes_ann	4510	3826	0.848337028824834	B.1.617.2
ORF7a	V82A	SampleC_freebayes_ann	4141	2302	0.555904370924897	B.1.617.2
ORF7a	T120I	SampleC_freebayes_ann	4981	2730	0.548082714314395	B.1.617.2
S	T19R	SampleC_freebayes_ann	2058	1448	0.703595724003887	B.1.617.2
S	L452R	SampleC_freebayes_ann	1753	1147	0.654306902452938	B.1.617.2
S	T478K	SampleC_freebayes_ann	1708	1088	0.637002341920375	B.1.617.2
S	D614G	SampleA_freebayes_ann	41	41	1	B.1.617.2
S	D614G	SampleB_freebayes_ann	15	15	1	B.1.617.2
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	B.1.617.2
S	P681R	SampleC_freebayes_ann	536	536	1	B.1.617.2
S	D950N	SampleC_freebayes_ann	949	368	0.387776606954689	B.1.617.2
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	B.1.617.2
ORF1b	G662S	SampleA_freebayes_ann	0	0	0	B.1.617.2
ORF1b	P1000L	SampleB_freebayes_ann	0	0	0	B.1.617.2
ORF8	D119I	SampleC_freebayes_ann	0	0	0	B.1.617.2
ORF8	del120/121	SampleA_freebayes_ann	0	0	0	B.1.617.2
S	G142D	SampleB_freebayes_ann	0	0	0	B.1.617.2
S	E156G	SampleC_freebayes_ann	0	0	0	B.1.617.2
S	del157/158	SampleA_freebayes_ann	0	0	0	B.1.617.2
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	B.1.617.2
ORF1b	G662S	SampleC_freebayes_ann	0	0	0	B.1.617.2
ORF1b	P1000L	SampleA_freebayes_ann	0	0	0	B.1.617.2
ORF8	D119I	SampleB_freebayes_ann	0	0	0	B.1.617.2
ORF8	del120/121	SampleC_freebayes_ann	0	0	0	B.1.617.2
S	G142D	SampleA_freebayes_ann	0	0	0	B.1.617.2
S	E156G	SampleB_freebayes_ann	0	0	0	B.1.617.2
S	del157/158	SampleC_freebayes_ann	0	0	0	B.1.617.2
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	B.1.617.2
ORF1b	G662S	SampleB_freebayes_ann	0	0	0	B.1.617.2
ORF1b	P1000L	SampleC_freebayes_ann	0	0	0	B.1.617.2
ORF8	D119I	SampleA_freebayes_ann	0	0	0	B.1.617.2
ORF8	del120/121	SampleB_freebayes_ann	0	0	0	B.1.617.2
S	G142D	SampleC_freebayes_ann	0	0	0	B.1.617.2
S	E156G	SampleA_freebayes_ann	0	0	0	B.1.617.2
S	del157/158	SampleB_freebayes_ann	0	0	0	B.1.617.2
S	N501Y	SampleA_freebayes_ann	6	6	1	P.1.1
S	N501Y	SampleB_freebayes_ann	4	4	1	P.1.1
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	P.1.1
S	D614G	SampleA_freebayes_ann	41	41	1	P.1.1
S	D614G	SampleB_freebayes_ann	15	15	1	P.1.1
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	P.1.1
N	P80R	SampleA_freebayes_ann	0	0	0	P.1.1
ORF1a	S1188L	SampleB_freebayes_ann	0	0	0	P.1.1
ORF1a	K1795Q	SampleC_freebayes_ann	0	0	0	P.1.1
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	P.1.1
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	P.1.1
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	P.1.1
ORF1b	E1264D	SampleA_freebayes_ann	0	0	0	P.1.1
ORF3a	S253P	SampleB_freebayes_ann	0	0	0	P.1.1
ORF8	E92K	SampleC_freebayes_ann	0	0	0	P.1.1
S	L18F	SampleA_freebayes_ann	0	0	0	P.1.1
S	T20N	SampleB_freebayes_ann	0	0	0	P.1.1
S	P26S	SampleC_freebayes_ann	0	0	0	P.1.1
S	D138Y	SampleA_freebayes_ann	0	0	0	P.1.1
S	R190S	SampleB_freebayes_ann	0	0	0	P.1.1
S	K417T	SampleC_freebayes_ann	0	0	0	P.1.1
S	E484K	SampleA_freebayes_ann	0	0	0	P.1.1
S	H655Y	SampleB_freebayes_ann	0	0	0	P.1.1
S	T1027I	SampleC_freebayes_ann	0	0	0	P.1.1
S	V1176F	SampleA_freebayes_ann	0	0	0	P.1.1
N	P80R	SampleB_freebayes_ann	0	0	0	P.1.1
ORF1a	S1188L	SampleC_freebayes_ann	0	0	0	P.1.1
ORF1a	K1795Q	SampleA_freebayes_ann	0	0	0	P.1.1
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	P.1.1
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	P.1.1
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	P.1.1
ORF1b	E1264D	SampleB_freebayes_ann	0	0	0	P.1.1
ORF3a	S253P	SampleC_freebayes_ann	0	0	0	P.1.1
ORF8	E92K	SampleA_freebayes_ann	0	0	0	P.1.1
S	L18F	SampleB_freebayes_ann	0	0	0	P.1.1
S	T20N	SampleC_freebayes_ann	0	0	0	P.1.1
S	P26S	SampleA_freebayes_ann	0	0	0	P.1.1
S	D138Y	SampleB_freebayes_ann	0	0	0	P.1.1
S	R190S	SampleC_freebayes_ann	0	0	0	P.1.1
S	K417T	SampleA_freebayes_ann	0	0	0	P.1.1
S	E484K	SampleB_freebayes_ann	0	0	0	P.1.1
S	H655Y	SampleC_freebayes_ann	0	0	0	P.1.1
S	T1027I	SampleA_freebayes_ann	0	0	0	P.1.1
S	V1176F	SampleB_freebayes_ann	0	0	0	P.1.1
N	P80R	SampleC_freebayes_ann	0	0	0	P.1.1
ORF1a	S1188L	SampleA_freebayes_ann	0	0	0	P.1.1
ORF1a	K1795Q	SampleB_freebayes_ann	0	0	0	P.1.1
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	P.1.1
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	P.1.1
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	P.1.1
ORF1b	E1264D	SampleC_freebayes_ann	0	0	0	P.1.1
ORF3a	S253P	SampleA_freebayes_ann	0	0	0	P.1.1
ORF8	E92K	SampleB_freebayes_ann	0	0	0	P.1.1
S	L18F	SampleC_freebayes_ann	0	0	0	P.1.1
S	T20N	SampleA_freebayes_ann	0	0	0	P.1.1
S	P26S	SampleB_freebayes_ann	0	0	0	P.1.1
S	D138Y	SampleC_freebayes_ann	0	0	0	P.1.1
S	R190S	SampleA_freebayes_ann	0	0	0	P.1.1
S	K417T	SampleB_freebayes_ann	0	0	0	P.1.1
S	E484K	SampleC_freebayes_ann	0	0	0	P.1.1
S	H655Y	SampleA_freebayes_ann	0	0	0	P.1.1
S	T1027I	SampleB_freebayes_ann	0	0	0	P.1.1
S	V1176F	SampleC_freebayes_ann	0	0	0	P.1.1
N	RG203KR	SampleA_freebayes_ann	14	14	1	P.1.2
N	RG203KR	SampleB_freebayes_ann	69	68	0.985507246376812	P.1.2
S	N501Y	SampleA_freebayes_ann	6	6	1	P.1.2
S	N501Y	SampleB_freebayes_ann	4	4	1	P.1.2
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	P.1.2
S	D614G	SampleA_freebayes_ann	41	41	1	P.1.2
S	D614G	SampleB_freebayes_ann	15	15	1	P.1.2
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	P.1.2
N	P80R	SampleA_freebayes_ann	0	0	0	P.1.2
ORF1a	S1188L	SampleB_freebayes_ann	0	0	0	P.1.2
ORF1a	K1795Q	SampleC_freebayes_ann	0	0	0	P.1.2
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	P.1.2
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	P.1.2
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	P.1.2
ORF1b	E1264D	SampleA_freebayes_ann	0	0	0	P.1.2
ORF3a	S253P	SampleB_freebayes_ann	0	0	0	P.1.2
ORF8	E92K	SampleC_freebayes_ann	0	0	0	P.1.2
S	L18F	SampleA_freebayes_ann	0	0	0	P.1.2
S	T20N	SampleB_freebayes_ann	0	0	0	P.1.2
S	P26S	SampleC_freebayes_ann	0	0	0	P.1.2
S	D138Y	SampleA_freebayes_ann	0	0	0	P.1.2
S	R190S	SampleB_freebayes_ann	0	0	0	P.1.2
S	K417T	SampleC_freebayes_ann	0	0	0	P.1.2
S	E484K	SampleA_freebayes_ann	0	0	0	P.1.2
S	H655Y	SampleB_freebayes_ann	0	0	0	P.1.2
S	T1027I	SampleC_freebayes_ann	0	0	0	P.1.2
S	V1176F	SampleA_freebayes_ann	0	0	0	P.1.2
N	P80R	SampleB_freebayes_ann	0	0	0	P.1.2
ORF1a	S1188L	SampleC_freebayes_ann	0	0	0	P.1.2
ORF1a	K1795Q	SampleA_freebayes_ann	0	0	0	P.1.2
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	P.1.2
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	P.1.2
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	P.1.2
ORF1b	E1264D	SampleB_freebayes_ann	0	0	0	P.1.2
ORF3a	S253P	SampleC_freebayes_ann	0	0	0	P.1.2
ORF8	E92K	SampleA_freebayes_ann	0	0	0	P.1.2
S	L18F	SampleB_freebayes_ann	0	0	0	P.1.2
S	T20N	SampleC_freebayes_ann	0	0	0	P.1.2
S	P26S	SampleA_freebayes_ann	0	0	0	P.1.2
S	D138Y	SampleB_freebayes_ann	0	0	0	P.1.2
S	R190S	SampleC_freebayes_ann	0	0	0	P.1.2
S	K417T	SampleA_freebayes_ann	0	0	0	P.1.2
S	E484K	SampleB_freebayes_ann	0	0	0	P.1.2
S	H655Y	SampleC_freebayes_ann	0	0	0	P.1.2
S	T1027I	SampleA_freebayes_ann	0	0	0	P.1.2
S	V1176F	SampleB_freebayes_ann	0	0	0	P.1.2
N	P80R	SampleC_freebayes_ann	0	0	0	P.1.2
ORF1a	S1188L	SampleA_freebayes_ann	0	0	0	P.1.2
ORF1a	K1795Q	SampleB_freebayes_ann	0	0	0	P.1.2
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	P.1.2
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	P.1.2
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	P.1.2
ORF1b	E1264D	SampleC_freebayes_ann	0	0	0	P.1.2
ORF3a	S253P	SampleA_freebayes_ann	0	0	0	P.1.2
ORF8	E92K	SampleB_freebayes_ann	0	0	0	P.1.2
S	L18F	SampleC_freebayes_ann	0	0	0	P.1.2
S	T20N	SampleA_freebayes_ann	0	0	0	P.1.2
S	P26S	SampleB_freebayes_ann	0	0	0	P.1.2
S	D138Y	SampleC_freebayes_ann	0	0	0	P.1.2
S	R190S	SampleA_freebayes_ann	0	0	0	P.1.2
S	K417T	SampleB_freebayes_ann	0	0	0	P.1.2
S	E484K	SampleC_freebayes_ann	0	0	0	P.1.2
S	H655Y	SampleA_freebayes_ann	0	0	0	P.1.2
S	T1027I	SampleB_freebayes_ann	0	0	0	P.1.2
S	V1176F	SampleC_freebayes_ann	0	0	0	P.1.2
N	RG203KR	SampleA_freebayes_ann	14	14	1	P.1
N	RG203KR	SampleB_freebayes_ann	69	68	0.985507246376812	P.1
S	N501Y	SampleA_freebayes_ann	6	6	1	P.1
S	N501Y	SampleB_freebayes_ann	4	4	1	P.1
S	N501Y	SampleC_freebayes_ann	1592	578	0.363065326633166	P.1
S	D614G	SampleA_freebayes_ann	41	41	1	P.1
S	D614G	SampleB_freebayes_ann	15	15	1	P.1
S	D614G	SampleC_freebayes_ann	3572	3570	0.999440089585666	P.1
N	P80R	SampleA_freebayes_ann	0	0	0	P.1
ORF1a	S1188L	SampleB_freebayes_ann	0	0	0	P.1
ORF1a	K1795Q	SampleC_freebayes_ann	0	0	0	P.1
ORF1a	S3675K	SampleA_freebayes_ann	0	0	0	P.1
ORF1a	del3676/3678	SampleB_freebayes_ann	0	0	0	P.1
ORF1b	P314L	SampleC_freebayes_ann	0	0	0	P.1
ORF1b	E1264D	SampleA_freebayes_ann	0	0	0	P.1
ORF3a	S253P	SampleB_freebayes_ann	0	0	0	P.1
ORF8	E92K	SampleC_freebayes_ann	0	0	0	P.1
S	L18F	SampleA_freebayes_ann	0	0	0	P.1
S	T20N	SampleB_freebayes_ann	0	0	0	P.1
S	P26S	SampleC_freebayes_ann	0	0	0	P.1
S	D138Y	SampleA_freebayes_ann	0	0	0	P.1
S	R190S	SampleB_freebayes_ann	0	0	0	P.1
S	K417T	SampleC_freebayes_ann	0	0	0	P.1
S	E484K	SampleA_freebayes_ann	0	0	0	P.1
S	H655Y	SampleB_freebayes_ann	0	0	0	P.1
S	T1027I	SampleC_freebayes_ann	0	0	0	P.1
S	V1176F	SampleA_freebayes_ann	0	0	0	P.1
N	P80R	SampleB_freebayes_ann	0	0	0	P.1
ORF1a	S1188L	SampleC_freebayes_ann	0	0	0	P.1
ORF1a	K1795Q	SampleA_freebayes_ann	0	0	0	P.1
ORF1a	S3675K	SampleB_freebayes_ann	0	0	0	P.1
ORF1a	del3676/3678	SampleC_freebayes_ann	0	0	0	P.1
ORF1b	P314L	SampleA_freebayes_ann	0	0	0	P.1
ORF1b	E1264D	SampleB_freebayes_ann	0	0	0	P.1
ORF3a	S253P	SampleC_freebayes_ann	0	0	0	P.1
ORF8	E92K	SampleA_freebayes_ann	0	0	0	P.1
S	L18F	SampleB_freebayes_ann	0	0	0	P.1
S	T20N	SampleC_freebayes_ann	0	0	0	P.1
S	P26S	SampleA_freebayes_ann	0	0	0	P.1
S	D138Y	SampleB_freebayes_ann	0	0	0	P.1
S	R190S	SampleC_freebayes_ann	0	0	0	P.1
S	K417T	SampleA_freebayes_ann	0	0	0	P.1
S	E484K	SampleB_freebayes_ann	0	0	0	P.1
S	H655Y	SampleC_freebayes_ann	0	0	0	P.1
S	T1027I	SampleA_freebayes_ann	0	0	0	P.1
S	V1176F	SampleB_freebayes_ann	0	0	0	P.1
N	P80R	SampleC_freebayes_ann	0	0	0	P.1
ORF1a	S1188L	SampleA_freebayes_ann	0	0	0	P.1
ORF1a	K1795Q	SampleB_freebayes_ann	0	0	0	P.1
ORF1a	S3675K	SampleC_freebayes_ann	0	0	0	P.1
ORF1a	del3676/3678	SampleA_freebayes_ann	0	0	0	P.1
ORF1b	P314L	SampleB_freebayes_ann	0	0	0	P.1
ORF1b	E1264D	SampleC_freebayes_ann	0	0	0	P.1
ORF3a	S253P	SampleA_freebayes_ann	0	0	0	P.1
ORF8	E92K	SampleB_freebayes_ann	0	0	0	P.1
S	L18F	SampleC_freebayes_ann	0	0	0	P.1
S	T20N	SampleA_freebayes_ann	0	0	0	P.1
S	P26S	SampleB_freebayes_ann	0	0	0	P.1
S	D138Y	SampleC_freebayes_ann	0	0	0	P.1
S	R190S	SampleA_freebayes_ann	0	0	0	P.1
S	K417T	SampleB_freebayes_ann	0	0	0	P.1
S	E484K	SampleC_freebayes_ann	0	0	0	P.1
S	H655Y	SampleA_freebayes_ann	0	0	0	P.1
S	T1027I	SampleB_freebayes_ann	0	0	0	P.1
S	V1176F	SampleC_freebayes_ann	0	0	0	P.1
