Table 1.

Overview of the sequencing data

Sample name	Abbrev.	Lane	Total number of reads	Accepted	Proportions	Number of reads longer than 16 nt, for which the 3’ adapter was trimmed
					Accepted	R	%R	NR	C
AfuCV-free replicate-1	CV_fr_r1	1	13,348,762	13,324,297	0.998	11,742,638	0.881	1,378,253	0.117
AfuCV-free replicate-2	CV_fr_r2	2	12,660,320	12,649,615	0.999	10,174,786	0.804	1,162,519	0.114
AfuCV-infected replicate-1	CV_inf_r1	1	18,854,816	18,820,738	0.998	16,692,438	0.886	1,542,300	0.092
AfuCV-infected replicate-2	CV_inf_r2	2	29,833,968	29,808,782	0.999	16,527,962	0.554	2,056,245	0.124
AfuTmV-1-free replicate-1	NK_fr_r1	1	23,496,360	23,451,950	0.998	18,143,950	0.773	1,934,229	0.106
AfuTmV-1-free replicate-2	NK_fr_r2	2	15,108,040	15,094,812	0.999	13,111,549	0.868	1,458,994	0.111
AfuTmV-1-infected replicate-1	NK_inf_r1	1	19,462,083	19,426,804	0.998	18,256,598	0.939	1,277,070	0.069
AfuTmV-1-infected replicate-2	NK_inf_r2	2	16,321,084	16,307,025	0.999	14,786,845	0.906	1,080,077	0.073
AfuPV-free replicate-1	PV_fr_r1	1	25,140,571	25,093,215	0.998	18,306,280	0.729	1,804,541	0.098
AfuPV-free replicate-2	PV_fr_r2	2	17,933,898	17,917,874	0.999	15,624,975	0.872	1,144,861	0.073
AfuPV-infected replicate-1	PV_inf_r1	1	43,825,751	43,744,985	0.998	41,804,128	0.955	1,748,249	0.041
AfuPV-infected replicate-2	PV_inf_r2	2	20,461,547	20,444,254	0.999	18,586,370	0.909	1,233,590	0.066

For each sample, we present the total number of reads, the number of accepted reads (reads without unassigned nucleotides, Ns), and the number reads longer than 16 nt, for which the 3’ adapter was found and trimmed. The redundant reads (R) are all accepted reads, the count of non-redundant reads (NR) is equivalent to the number of unique reads; the complexity (C) is the ratio of NR to R reads and can vary between 0 and 1. Values close to 0 indicate the presence of a small number of very abundant sequences and values close to 1 indicate the presence of many sequences, with low abundances