Table 2. The coverages and stutter ratios of the MiSeq-detected SSRs in rice varieties A–H.

Varieties SSRs	A	B	C	D	E	F	G	H	Average	Standard deviation
Total reads (M)	2.12	2.31	2.74	2.42	2.53	2.23	3.11	2.33	2.35	0.47
Consistent reads (M) 1	1.56	1.73	1.98	1.78	1.87	1.55	2.34	1.69	1.81	0.26
Reads mapped to SSR amplicons (M)	1.17	1.40	1.61	1.35	1.30	1.06	1.73	1.40	1.38	0.22
Detected SSRs	2480	2290	2476	2334	2297	2480	2597	2468	2427.75	108.83
Detected SSRs (%)2	79.87	73.75	79.74	75.17	73.98	79.87	83.64	79.48	78.19	3.51
Coverage per detected SSR	508.90	646.83	669.96	629.30	597.77	426.90	687.18	590.68	594.69	87.57
Stutter ratio per detected SSR (%)	16.07	12.83	15.96	14.31	14.95	16.18	17.27	14.42	15.25	1.40
SSRs with coverage ≥10× and stutter ratio ≤0.5	1874	1756	1920	1755	1753	1874	1989	1922	1855.38	90.71
SSRs with coverage ≥10× and stutter ratio ≤0.5 (%)3	75.56	76.68	77.54	75.19	76.32	75.56	76.59	77.88	76.42	0.96

¹Consistent reads are the MiSeq reads with identical forward and backward sequences.

²Detected SSRs (%) = Detected SSRs/3105.

³SSRs with coverage ≥10× and stutter ratio ≤0.5 (%) = SSRs with coverage ≥10× and stutter ratio ≤0.5/Detected SSRs.