File	Total Reads	Aligned Reads	Unaligned Reads	Ambiguously Aligned Reads	No Genomic Sequence	Duplicate Reads (removed)	Unique Reads (remaining)	Total Cs	Methylated CpGs	Unmethylated CpGs	Methylated chgs	Unmethylated chgs	Methylated CHHs	Unmethylated CHHs
CF01-CM01-Zygote_1_val_1_bismark_bt2_pe.bam	32066854	858885	30767490	440479	0	210346	648539	9592319	245311	960481	36410	1744749	189538	6415830
CF08-CM04-Larvae_1_val_1_bismark_bt2_pe.bam	53982337	122004	53789321	71012	0	53993	68011	1537327	39593	157203	6049	281012	60758	992712
EF05-EM05-Zygote_1_val_1_bismark_bt2_pe.bam	121419064	1511928	118808705	1098427	4	483639	1028289	11482823	210441	1254596	40675	2100433	247338	7629340
CF06-CM02-Larvae_1_val_1_bismark_bt2_pe.bam	112960848	4026393	107073752	1860702	1	1089544	2936849	55382483	2082657	5605811	655136	10789762	2673926	33575191
EF04-EM04-Zygote_1_val_1_bismark_bt2_pe.bam	156150111	1336863	153935583	877660	5	455225	881638	11268981	276673	1223939	78148	2082104	368161	7239956
CF08-CM05-Larvae_1_val_1_bismark_bt2_pe.bam	80659282	412628	80081227	165427	0	364028	48600	1348903	28830	138095	3114	237959	23597	917308
EF08-EM04-Larvae_1_val_1_bismark_bt2_pe.bam	118471780	9230903	104345599	4895273	5	2555757	6675146	123737866	3993919	14870836	616813	26656448	2488960	75110890
CF03-CM03-Zygote_1_val_1_bismark_bt2_pe.bam	131835534	7402799	120499119	3933611	5	1994208	5408591	78774460	2321907	7935090	412006	15253827	2100421	50751209
EF03-EM03-Zygote_1_val_1_bismark_bt2_pe.bam	133963220	3845039	128086986	2031186	9	1112953	2732086	38297973	1116326	3629057	257347	7040500	1271820	24982923
CF03-CM05-Larvae_1_val_1_bismark_bt2_pe.bam	114571678	7194757	103941241	3435675	5	1800185	5394572	120110096	3847165	14421825	813604	25236051	3041491	72749960
EF02-EM02-Zygote_1_val_1_bismark_bt2_pe.bam	144204708	7504501	132171375	4528823	9	2069445	5435056	89276272	2182076	11059712	304383	18827254	1312542	55590305
CF06-CM01-Zygote_1_val_1_bismark_bt2_pe.bam	148147821	6104692	138951762	3091366	1	1599419	4505273	66662481	2088106	6662588	440880	12653542	2036016	42781349
CF04-CM04-Zygote_1_val_1_bismark_bt2_pe.bam	129451230	8113086	117441488	3896648	8	2713370	5399716	92264525	2549416	9708052	456227	18032088	2059874	59458868
EF05-EM01-Larvae_1_val_1_bismark_bt2_pe.bam	106370434	5938013	97546916	2885501	4	1690383	4247630	95267033	3069592	11597576	336970	20282830	1336967	58643098
EF03-EM05-Larvae_1_val_1_bismark_bt2_pe.bam	137182959	6857979	127216119	3108856	5	1676687	5181292	108661595	3456033	12388694	797458	22093122	3125650	66800638
EF03-EM04-Larvae_1_val_1_bismark_bt2_pe.bam	133064817	8132878	120890827	4041100	12	2298543	5834335	112079074	3876781	12144108	1168529	22699773	4227120	67962763
CF05-CM05-Zygote_1_val_1_bismark_bt2_pe.bam	145974867	8082146	134010787	3881926	8	2326615	5755531	103112507	3319433	11352927	633150	21160637	2601473	64044887
EF01-EM01-Zygote_1_val_1_bismark_bt2_pe.bam	123296503	4622178	116597721	2076603	1	1224190	3397988	61553708	2184527	6021875	651091	11755786	2779461	38160968
EF07-EM03-Larvae_1_val_1_bismark_bt2_pe.bam	129568902	10742870	113779883	5046138	11	3558846	7184024	159451915	4422956	18546986	594685	32757381	2612632	100517275
CF08-CM03-Zygote_1_val_1_bismark_bt2_pe.bam	146878473	5679883	138145424	3053159	7	2160282	3519601	46665479	1167793	4197031	263113	7940977	1503982	31592583
EF06-EM02-Larvae_1_val_1_bismark_bt2_pe.bam	116000867	8191373	104044639	3764848	7	2311514	5879859	121770375	3941730	14550695	620122	25954395	2338962	74364471
CF01-CM02-Larvae_1_val_1_bismark_bt2_pe.bam	134132252	11518606	116703665	5909955	26	2987570	8531036	166507980	5109892	20734766	672493	36186923	2770709	101033197
CF02-CM02-Zygote_1_val_1_bismark_bt2_pe.bam	207659794	5600693	198926145	3132946	10	2317700	3282993	40701548	1064052	3560800	334337	6837924	1827600	27076835
EF04-EM05-Larvae_1_val_1_bismark_bt2_pe.bam	141012810	11898925	123629483	5484390	12	3505385	8393540	195860225	5452119	23988980	545497	41201302	2265245	122407082
CF03-CM04-Larvae_1_val_1_bismark_bt2_pe.bam	122527976	14663031	100661495	7203443	7	8414507	6248524	147780068	4066880	17065806	431908	29752182	1796774	94666518
EF06-EM06-Larvae_1_val_1_bismark_bt2_pe.bam	161042344	7039640	150781448	3221250	6	5792109	1247531	21568606	614301	2065729	162840	3902535	763533	14059668
CF07-CM02-Zygote_1_val_1_bismark_bt2_pe.bam	213314972	5882055	204298035	3134880	2	2139593	3742462	59344749	1531826	6064117	199785	11444666	1238650	38865705
EF06-EM01-Larvae_1_val_1_bismark_bt2_pe.bam	142691881	11411796	126148066	5131989	30	3032216	8379580	195501359	5244180	23458238	657955	39834976	2800306	123505704
CF05-CM02-Larvae_1_val_1_bismark_bt2_pe.bam	164930959	13862701	144234025	6834201	32	3896108	9966593	212959978	6051797	26368561	603759	45372293	2690876	131872692
EF08-EM03-Larvae_1_val_1_bismark_bt2_pe.bam	163422108	16232543	138834434	8355106	25	7330639	8901904	189554589	5695591	22908938	560047	39962633	2377590	118049790
EF05-EM06-Larvae_1_val_1_bismark_bt2_pe.bam	198669235	15831792	176884677	5952751	15	8704128	7127664	205782117	6710946	21320580	3301439	36225707	13524812	124698633
EF07-EM01-Zygote_1_val_1_bismark_bt2_pe.bam	241124954	6276696	231281319	3566918	21	3460494	2816202	40107908	833699	4045377	113290	7197973	733956	27183613