Table 1. Classification of pathogen-specific sequence reads from symptomatic and non-symptomatic samples.

Category of sequence reads	Reads from ribo-depletedcDNA library		Reads from dual-depletedcDNA library
	Symptoms	No Symptoms	Symptoms	No Symptoms
Reads mapped to specific virus
GRLaV	15,036	0	406	0
GFLV	14,383	0	978	0
GRSPaV	662	1,353	42	68
Reads mapped to specific viroid
GYSVd-1	13,914	9,004	987	490
CEYVd	1,605	152	5	10
CEVd	856	86	6	2
HpSVd	1,964	2,980	164	185
Other*	5,568	2,693	644	1,604
Total	53,988	16,268	3,232	2,539

GRLaV = Grapevine redleaf-associated virus, GRSPaV = Grapevine rupestris stem pitting-associated virus, GFLV = Grapevine fanleaf virus, HpSVd = Hop stunt viroid, GYSVd-1 = Grapevine yellow speckle viroid 1, CEVd = Citrus exocortis viroid, CEYVd = Citrus exocortis Yucatan viroid.

^*Reads mismapped to virus- or viroid-like sequences.

Classification and abundance of high-throughput sequence reads obtained from ribo-depleted and dual-depleted cDNA libraries were determined by mapping the reads onto the virus/viroid database using mapping software BWA 0.6.