Table 1.

Statistics for Bisulphite Sequencing of All Tissues and Stages

	Sperm	Egg	2 to 16	64	256	Sphere	Muscle
Alignments	481,791,530	486,728,832	912,758,760	512,417,692	696,177,617	405,903,980	681,903,486
Alignments passing filters	303,464,480	227,823,167	243,963,809	200,264,006	217,119,875	266,359,218	393,924,207
Total base pairs passing all filters	24,963,074,472	14,920,822,820	16,001,950,219	15,377,294,129	18,047,036,957	24,451,509,179	33,145,552,386
Read coverage	17.67	10.56	11.33	10.89	12.78	17.31	23.47
Conversion rate, %	98.99	98.67	99.70	99.76	96.58	99.82	99.57
mCG/(C+mC), %	18.65	10.77	10.18	9.01	13.20	17.08	12.63
mNonCG/(C+mC), %	1.39	1.98	0.40	0.35	6.85a	0.39	0.60
mCG/(C+mC) + mitochondrial DNA, %	19.22	8.17	5.30	6.66	13.45	17.19	13.14
mCG/(CG+mCG)	0.95	0.75	0.83	0.83	0.91	0.94	0.90

The data describe, for each tissue/stage, the number of alignments (or base pairs) used in the analysis (rows 1–3). See Extended Experimental Procedures for information and thresholds used in filtering alignments. Read coverage (row 4) refers to genome equivalents. Read coverage calculations exclude chrM. Conversion rate (row 5) refers to the extent (in percent) of C > T conversion by bisulfite treatment. Unmethylated Lambda DNA was used as an internal control to determine bisulphite conversion rate. Rows 6–9 provide different measures (indicated) at calculating cytosine methylation in CG and non-CG contexts. See also Figure S2 and Table S3.

^aMajority due to nonconversion.