TABLE 5.

Data characterizing for each segment the quantity and quality of the sequences obtained for isolates R1959/2007 and R1372/2007

Isolate	Segment/gene	Median depthc	Coding sequencea			Overall sequenceb
			Lengthd	% Coveragee	No. (%) of Q40+ basesf	Length	% Coverage	No. (%) of Q40+ bases
R1959	1/PB2	166	2,280	100.00	2,273 (99.69)	2,332	99.62	2,325 (99.70)
	2/PB1	129	2,274	100.00	2,269 (99.78)	2,303	98.38	2,292 (99.52)
	3/PA	92	2,151	100.00	2,141 (99.54)	2,201	98.57	2,190 (99.50)
	4/HA	64	1,707	100.00	1,703 (99.77)	1,748	98.26	1,744 (99.77)
	5/NP	92	1,497	100.00	1,494 (99.80)	1,534	98.02	1,526 (99.48)
	6/NA	73	1,350	100.00	1,349 (99.93)	1,401	100.00	1,393 (99.43)
	7/M	129	759	100.00	759 (100.00)	892	86.85	892 (100.00)
	8/NS	60	678	100.00	677 (99.85)	870	99.43	869 (99.89)
R1372	1/PB2	62	2,250	98.68	2,245 (99.78)	2,274	97.14	2,269 (99.78)
	2/PB1	47	2,275	99.96	2,265 (99.56)	2,303	98.38	2,289 (99.39)
	3/PA	32	2,097	96.37	2,080 (99.19)	2,097	93.91	2,080 (99.19)
	4/HA	18	1,707	100.00	1,678 (98.30)	1,748	98.26	1,718 (98.28)
	5/NP	28	1,405	93.65	1,390 (98.93)	1,415	90.42	1,399 (98.87)
	6/NA	13	1,187	87.93	1,160 (97.73)	1,187	84.91	1,160 (97.73)
	7/M	25	759	100.00	756 (99.60)	918	89.39	912 (99.35)
	8/NS	28	678	100.00	677 (99.85)	853	97.49	850 (99.65)

^aOnly the coding part in the de novo assembly is considered.

^bThe complete sequences of the segments in the assembly are considered.

^cMedian of the overall sequence depth(the number of times that each nucleotide was sequenced).

^dLength of the assembly covering the portion of the segment considered.

^ePercent coverage of the reference sequence (the reference sequences are as described in Table 3 for isolate R747/2006).

^fNumber of bases with a quality score of ≥40 (Q40+), i.e., with a probability of ≥99.99% for the individual bases, and the percentage of bases with a quality score of ≥40 in the sequence portion considered.