Table 3.

Overview of sequencing read counts in four sRNA libraries. TCG, constructed from DBA Aurora CG seedlings. TWH, constructed from DBA Aurora WH seedlings. SCG, constructed from L6 CG seedlings. SWH, constructed from L6 WH seedlings. Clean reads may not be equal to raw reads minus all the filter type reads, as there could be overlapped sequences between mRNA, Rfam and Repeats filters.

Read Type	TCG		TWH		SCG		SWH
	Total Reads	Unique Reads	Total Reads	Unique Reads	Total Reads	Unique Reads	Total Reads	Unique Reads
Raw reads	20,042,833	8,293,425	20,900,186	8,593,357	24,262,343	8,865,724	18,786,468	7,221,909
3ADT & Length filter	6,000,364	1,418,893	5,651,835	1,475,235	7,669,010	1,832,961	6,589,933	1,676,502
Junk reads	92,538	68,473	101,066	73,192	111,339	79,088	76,371	56,322
Rfam - rRNA	215,716	5440	228,715	5378	308,312	6809	266,089	7444
Rfam - tRNA	230,895	2119	215,340	2207	248,091	2853	310,937	3964
Rfam - snoRNA	9600	393	9813	396	10,886	363	8009	304
Rfam - snRNA	2364	181	2581	194	3250	264	3580	215
Other Rfam RNA	13,680	733	14,276	706	19,445	886	17,165	893
mRNA	878,039	23,905	915,468	25,170	1,090,076	26,584	798,629	20,880
Repeats	6104	186	6073	193	9312	265	7704	243
Clean reads	12,631,656	6,773,722	13,795,248	7,011,288	14,830,872	6,916,493	10,781,672	5,456,127