Table 1.

Quantitation of specific virus reads and sequence coverage in virus stocks.

Virus	Virus titer (EID50/ml)	Gene segments	Coverage (%)	Mean depth of coverage	SD	Assembled reads/total paired readsa	Q30
							(%)
AIV H5N2	106	PB2	100	12,180.5	12,784.2	112,856	96.5
A/turkey/Minnesota/15–012582-1/2015		PB1	98.9b	4685.6	4207.6	46,495	96.5
		PA	100	7385.4	7727.8	79,192	87.4
		HA	100	14,846.5	12,410.4	102,233	96.4
		NP	100	1917.1	1125.9	20,574	75.9
		NA	100	13,563.2	11,913.8	92,618	94
		M	100	8656.1	6618.8	37,642	93.7
		NS	100	3800.7	2176.8	14,017	97
		Genome				505,627/ 718,922	N/A
AIV H5N1	105.9	PB2	98.1c	200.4	92.7	3007	95.8
A/duck/Vn/NCVD-672/2011		PB1	100	62.7	46.3	972	96.3
		PA	100	91.4	63.5	1296	94.9
		HA	100	1330.9	817.2	15,448	67.4
		NP	100	409.6	460.4	4233	86.7
		NA	98.7d	780.2	640.8	7302	95.7
		M	100	1378.6	1061.9	9142	95.7
		NS	100	149.9	79.6	758	95.8
		Genome				163,661/ 421,418	N/A
NDV	107	NP	100	625.6	203.9
Lasota vaccine strain		P	100	1898.2	1025.1
		M	100	4280.4	2819.7
		F	100	3513.5	1078.1
		HN	100	23,703.1	20,025.1
		L	100	6408.3	3946.8
		Genome	100	7151	10,584.4	388,022/ 847,390	94.8
	106.1	N	100	24,060	8087.3
		5b	100	9269.7	3608.6
IBV		5a	100	2272.4	990.8
Ark99		M	100	490.6	114
		3c	100	597.9	49.9
		3b	100	951.8	214.6
		3a	100	1767.1	160.7
		S	100	1281.7	958.4
		ORF1ab	100	6382.4	15,046.8
		Genome	100	6503.4	13,883.2	576,259/ 772,020	96.6

SD, standard deviation; N/A, not applicable.

^aThe numbers of assembled sequencing reads to a reference genome.

^bGaps at nucleotide position 588–613.

^cGaps at nucleotide position 1–44.

^dGaps at nucleotide position 1–17.