Table 1:

Summary of minor variant mutations analysis of PB2 D701 Cluster sequences

Chromosome / Segment	Genome position	Referen ce allele	Alternative allele	Alternative allele frequency / Position (Annotate allele)			Allele effect	Allele impact	CDS variation	CDS length	Protein variation	Comments
				240524-2/2023	240265/2023	240270-1/2023
OQ352545.1. / Seg 1 (PB2)	1590	T	A	78,32 / 535 (A)	76,92 / 65 (A)	75,61 / 123 (A)	synonymous variant	LOW	1563T>A	2280	T521T	Present on 78 sequences
	2128	G	A	52,94 / 527 (A)	70,88 / 1092 (A)	65,19 / 135 (A)	missense variant	MODERATE	2101G>A	2280	D701N	Only on D701N cluster sequences
	2160	T	C	65,08 / 524 (C)	87,35 / 1289 (C)	90,37 / 135 (C)	synonymous variant	LOW	2133T>C	2280	N711N	Present on 39 sequences
OQ352546.1 / Seg 2 (PB1)	96	A	G	100 / 3 (G)	73,53 / 170 (G)	86,15 / 65 (G)	synonymous variant	LOW	69A>G	2274	P23P	Present on 78 sequences
	705	A	G	100 / 3 (G)	78,46 / 65 (G)	85,94 / 65 /G)	synonymous variant	LOW	678A>G	2274	T226T	Present on 78 sequences
	723	G	A	33,33 / 3 (A)	78,12 / 64 (A)	84,38 / 64 (A)	synonymous variant	LOW	696G>A	2274	E232E	Present on 78 sequences
	1570	T	G	75 / 4 (G)	76,27 / 118 (G)	81,82 /154 (G)	missense variant	MODERATE	1543T>G	2274	S515A	Present on 40 sequences
OQ352547.1 / Seg 3 (PA)	150	A	G	77,39 / 115 (G)	77,39 / 115 (G)	79,37 / 63 (G)	synonymous variant	LOW	126A>G	2151	L42L	Present on 33 sequences
	1692	A	G	73,39 / 124 (G)	70,63 / 126 (G)	73,13 / 67 (G)	synonymous variant	LOW	1668A>G	2151	Q556Q	Present on 37 sequences
	150	A	G	77,39 / 115 (G)	77,39 / 115 (G)	79,37 / 63 (G)	synonymous variant	LOW	126A>G	759	L42L	Present on 37 sequences
OQ352548.1 / Seg 4 (HA)	610	T	C	89,97 / 3130 (C)	88,94 / 461 (C)	88,19 / 415 (C)	synonymous variant	LOW	582T>C	1704	I194I	Present on D701 cluster and 3 more samples sequences
OQ352549.1 / Seg 5 (NP)	401	T	C	79,47 / 5255 (C)	76,75 / 1045 (C)	77,12 / 813 (C)	missense variant	MODERATE	356T>C	1497	I119T	Present on D701 cluster and 4 more samples sequences
	714	C	T	63,24 / 5283 (T)	60,36 / 1047 (T)	62,41 / 814 /T)	synonymous variant	LOW	669C>T	1497	C223C	Only on D701N cluster sequences
OQ352551.1 / Seg 7 (M)	691	T	C	47,79 / 15659 (C)	59,61 / 3442 (C)	59,31 /3728 (C)	synonymous variant	LOW	666T>C	759	H222H	Only on D701N cluster sequences
	691	T	C	47,79 / 15659 (C)	59,61 / 3422 (C)	59,31 /3728 (C)	intron variant	MODIFIER	27–49T>C	294		Only on D701N cluster sequences
OQ352552.1 / Seg 8 (NS)	102	G	A	52,86 / 32303 (A)	64,3 / 372 (A)	62,81 / 5230 (A)	intron variant	MODIFIER	30+46G>A	366		Present on 44 sequences
	703	T	C	70,9 / 33304 (C)	83 / 3700 (C)	82,62 / 5312 (C)	synonymous variant	LOW	205T>C	366	L69L	Present on D701 cluster and one more Se lion sequence
	102	G	A	52,86 / 32302 (A)	64,3 / 3712 (A)	62,81 / 5230 (A)	missense variant	MODERATE	76G>A	693	E26K	Present on 44 sequences
	703	T	C	70,9 / 33304 (C)	83 / 3700 (C)	82,62 / 5312 (C)	missense variant	MODERATE	677T>C	693	I226T	Present on D701 cluster and Sea lion sequences