Table 2.

Quantitation of specific virus reads and coverage in the clinical samples.

Virus	Virus titer (EID50/ml)	Gene segment	Coverage (%)	Mean depth of coverage	SD	Assembled reads/total paired readsa	Q30
							(%)
AIV H9N2	107.7	PB2	100	349	241	4879	93.7
A/chicken/Jordan/13/2003		PB1	100	100	263.7	139.8	94.4
		PA	100	71.6	27.6	909	94.2
		HA	100	611.9	473.2	5959	94.1
		NP	100	46.2	32.7	1024	94.4
		NA	100	1092.4	981.7	9617	94.5
		M	100	545.4	425.2	3214	93.4
		NS	85.4b	3.1	2	17	90.5
		Genome				29,217/ 530,908	N/A
NDV	107.1	NP	82.1	2.7	2.0
chicken/Jordan/17/2004		P	100	21.3	13.4
		M	99.3	16.7	8.0
		F	100	33.2	15.8
		HN	100	19.5	7.2
		L	99.7	21.3	19.6
		Genome	94.9c	18.1	16.3	1378/ 534,158	92.1
NDVf chicken/Jordan/15/2004	107.2	NP	90.1	2.1	2.6
		P	100	100	34.1
		M	100	536.1	528
		F	100	48.8	17.3
		HN	100	281.6	280.6
		L	99.98	60	50.9
		Genome	98.1d	874.3	3063	114,992/ 608,250	93.4
IBVf Jordan/Mass/15/2004	106.2	N	100	176	43.9
		5b	100	100	69.1
		5a	100	45.9	6.9
		M	100	24	5.1
		3c	100	40.5	7.7
		3b	100	73.9	14.9
		3a	100	118	7.3
		S	100	68	61.7
		ORF1ab	98.5	23.7	31.7
		Genome	98.8e	2468	6728	118,763/ 608,250	98

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

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

^bGaps at nucleotide position 1–65; 603–763; 809–838.

^cGaps at nucleotide position 1–196; 1148–1237;1419–1750; 3085–3316; 15,103– 15,190.

^dGaps at nucleotide position 1–979; 14,939– 14,979.

^eGaps at nucleotide position 1–302; 15,059– 15,063; 15,113– 15,213; 27,622– 27,641.

^fMix viral infections obtained in a single reaction from clinical sample.