Table 1.

BS-Seq samples analyzed in this study

DOI: http://dx.doi.org/10.7554/eLife.00354.003

Sample	Description	Raw reads	Uniquely mapping reads	Coverage (X)	CG error rate	CHG error rate	CHH error rate
1	WT2003	231568902	100572780	13.5178	0.0176	0.0122	0.0099
2	WT2007	203541357	104376988	14.0292	0.0107	0.0087	0.0082
3	WT2011	187803109	84301904	11.3309	0.0158	0.0095	0.0065
4	T2-PiZt-11-R	229650259	118710094	15.9557	0.0139	0.0099	0.0069
5	T2-PiZt-11-S	263329602	136471411	18.3429	0.0101	0.0096	0.0076
6	T4-PiZt-11-R	270670871	131056700	17.6151	0.0117	0.0100	0.0074
7	T4-PiZt-11-S	252150298	128467721	17.2672	0.0096	0.0076	0.0074
8	T6-PiZt-11-R	237280137	121966745	16.3934	0.0105	0.0096	0.0064
9	T6-Pi9-R	204752699	86995742	11.6930	0.0106	0.0093	0.0050
10	T6-Spin1i-1-R	215451022	90468236	12.1597	0.0113	0.0088	0.0061
11	T2-PiZt-839-8-R (non functional PiZt)	238730281	117471332	15.7892	0.0129	0.0079	0.0056
12	T2-PiZt-839-8-S (non functional PiZt)	211006119	106172872	14.2705	0.0178	0.0129	0.0095
13	WT Callus 1	217121522	96145279	12.9228	0.0185	0.0178	0.0070
14	WT Callus 2	199261493	82617643	11.1045	0.0232	0.0222	0.0084
15	WT regenerated from tissue culture 1	218008835	116367626	15.6408	0.0170	0.0155	0.0078
16	WT regenerated from tissue culture 2	225202113	97905142	13.1593	0.0262	0.0206	0.0093
17	WT regenerated from tissue culture 3	252306428	106544735	14.3205	0.0194	0.0160	0.0073
18	WT2011 (replicate)	253971827	118140062	15.8790	0.0172	0.0148	0.0086

Number of raw sequencing reads, number of uniquely mapping reads (post-removal of identical reads), genome coverage (rice genome size = 372 Mb), and error rates are listed. DNA methylation levels of the chloroplast genome were used to estimate error rates. Samples 1–12 and samples 13–18 were prepared separately. “R” and “S” correspond to plants that either contain the transgene (R) or plants in which the transgene was segregated away (S).