A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus

BMC Genomics

Table 2 Detailed statistics of SARS-CoV-2 genome assembly after SISPA amplification coupled with Illumina sequencing

Viral titre (pfu/ml)	Ct value	Gene	Reference assembly			De novo assembly
Viral titre (pfu/ml)	Ct value	Gene	The percentage (%) of genome covered	Average	SD	De novo assembly
				overage depth
2.6 × 10⁶	12.22	orf1ab	100	21,439.7	20,844.3
		S	100	2560.8	776.9
		orf3a	100	3203.5	606
		E	100	2630	446.3
		M	100	3114.5	976.3
		orf6	100	4874	233.5
		orf7a	100	8860.4	2037.3
		orf7b	100	13,001.8	298
		orf8	100	13,765.3	821.8
		N	100	19,803.9	3615.6
		orf10	100	10,446.2	2341.1
Genome (including non-coding regions)			100	17,104.6	19,211.0	Y
2.6 × 10⁵	15.99	orf1ab	100	9651.8	10,201.6
		S	100	990	584.9
		orf3a	100	1070.9	420
		E	100	690.3	258.5
		M	100	391.5	162.5
		orf6	100	474.8	123.6
		orf7a	100	2244.3	667.2
		orf7b	100	3182.9	60.7
		orf8	100	2892.8	434.7
		N	100	1831.2	434.2
		orf10	100	1991	351.1
Genome (including non-coding regions)			100	7246.3	9438.9	Y
2.6 × 10⁴	18.99	orf1ab	100	6192.5	5919.4
		S	100	962.4	434.5
		orf3a	100	1075.7	404.4
		E	100	711.6	283.4
		M	100	539.8	218.6
		orf6	100	460.1	112
		orf7a	100	2256	788.2
		orf7b	100	3455.9	34.8
		orf8	100	3153	308.7
		N	100	2635.3	401.4
		orf10	100	1615.3	346.6
Genome (including non-coding regions)			100	4812.3	5484.8	Y
2.6 × 10³	22.4	orf1ab	100	1100	1099.9
		S	100	133.7	113.5
		orf3a	100	62	28.4
		E	100	61	19.1
		M	100	75.5	62.7
		orf6	100	76.1	24.3
		orf7a	100	390.8	116.6
		orf7b	100	423.1	24.4
		orf8	100	257.1	74.7
		N	100	147.7	56.4
		orf10	100	153.3	12.4
Genome			100	826	1028.4	Y
(including non-coding regions)
2.6 × 10²	25.34	orf1ab	95.5	78.3	123.7
		S	84.5	12	9.6
		orf3a	0	0.5	0.8
		E	0	0.6	0.7
		M	0	0	0
		orf6	0	0.4	0.6
		orf7a	100	10.4	3.5
		orf7b	100	6.8	1.1
		orf8	100	12.2	2.1
		N	100	21.7	10.8
		orf10	100	25.6	3.9
Genome			89.6	59	109.1	N
(including non-coding regions)
	29.34	N/A				N
	32.34	N/A				N
	35.04	N/A				N

ISSN: 1471-2164