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
0501_R1_bismark_bt2_pe.bam	100000	59640	30009	10351	0	3083	56557	1859705	29965	193629	2901	301308	13262	1318640
0502_R1_bismark_bt2_pe.bam	100000	59284	30449	10267	0	2824	56460	1880911	29142	193905	3310	305640	13974	1334940
0503_R1_bismark_bt2_pe.bam	100000	59416	30587	9997	0	2994	56422	1849861	31012	187357	3012	296163	14206	1318111
3501_R1_bismark_bt2_pe.bam	100000	60904	28435	10661	0	3124	57780	1860250	27690	194133	3151	298113	13309	1323854
3502_R1_bismark_bt2_pe.bam	100000	61008	28396	10596	0	3289	57719	1914887	28773	199776	3084	310413	12967	1359874
3503_R1_bismark_bt2_pe.bam	100000	57332	32794	9874	0	2434	54898	1846095	29111	190000	2883	297786	12836	1313479
5201_R1_bismark_bt2_pe.bam	100000	60895	28803	10302	0	3072	57823	1739031	25095	178413	2450	273483	10982	1248608
5202_R1_bismark_bt2_pe.bam	100000	60899	28595	10505	1	2956	57943	1975314	28144	210593	3074	323279	13166	1397058
5203_R1_bismark_bt2_pe.bam	100000	58371	31612	10017	0	2728	55643	1813834	29295	186579	3166	290961	14301	1289532
5901_R1_bismark_bt2_pe.bam	100000	59788	29986	10226	0	3275	56513	1891864	30700	199778	3083	309087	13000	1336216
5902_R1_bismark_bt2_pe.bam	100000	60658	29074	10268	0	3179	57479	1978606	28775	207515	3057	321019	13217	1405023
5903_R1_bismark_bt2_pe.bam	100000	59448	30289	10263	0	2372	57076	1980266	29502	213177	4260	323900	18399	1391028
zr3534_10_R1_bismark_bt2_pe.bam	100000	61864	21587	16549	0	6408	55456	1340768	17015	157144	1048	232950	4335	928276
zr3534_1_R1_bismark_bt2_pe.bam	100000	61618	22474	15908	0	6726	54892	1330789	17210	154648	1071	229591	4667	923602
zr3534_2_R1_bismark_bt2_pe.bam	100000	61056	22398	16546	0	6107	54949	1337084	16934	156596	1053	230643	4861	926997
zr3534_3_R1_bismark_bt2_pe.bam	100000	60805	23295	15900	0	5850	54955	1361137	20085	153239	1230	233513	5181	947889
zr3534_4_R1_bismark_bt2_pe.bam	100000	61751	22130	16118	1	6492	55259	1334307	18547	153522	1068	230168	4983	926019
zr3534_5_R1_bismark_bt2_pe.bam	100000	61435	22294	16271	0	6349	55086	1321450	18706	149852	1142	227304	4868	919578
zr3534_6_R1_bismark_bt2_pe.bam	100000	60946	23409	15645	0	6386	54560	1329087	17277	152699	1077	227992	4605	925437
zr3534_7_R1_bismark_bt2_pe.bam	100000	61281	23002	15717	0	5803	55478	1350779	17175	153801	1062	231013	5015	942713
zr3534_8_R1_bismark_bt2_pe.bam	100000	61749	21889	16362	0	7118	54631	1286222	16614	147209	991	220589	4536	896283
zr3534_9_R1_bismark_bt2_pe.bam	100000	61884	21378	16737	1	6157	55727	1352824	17147	158036	1109	235705	4655	936172
zr3644_10_R1_bismark_bt2_pe.bam	100000	61153	21890	16956	1	4006	57147	1367044	18292	158774	1099	236251	4850	947778
zr3644_11_R1_bismark_bt2_pe.bam	100000	60960	21931	17108	1	4074	56886	1358219	17603	157564	1113	234678	5036	942225
zr3644_12_R1_bismark_bt2_pe.bam	100000	61367	22024	16609	0	3889	57478	1353399	16221	152373	1001	225562	4482	953760
zr3644_13_R1_bismark_bt2_pe.bam	100000	61792	21880	16328	0	4450	57342	1406264	18175	160953	1149	241126	5038	979823
zr3644_14_R1_bismark_bt2_pe.bam	100000	62088	21390	16521	1	4054	58034	1392769	20439	156912	1189	238595	4943	970691
zr3644_15_R1_bismark_bt2_pe.bam	100000	61418	21905	16677	0	3982	57436	1385235	19228	157318	1169	237701	4747	965072
zr3644_16_R1_bismark_bt2_pe.bam	100000	61736	20553	17711	0	4307	57429	1314284	17404	152417	1122	227151	4762	911428
zr3644_17_R1_bismark_bt2_pe.bam	100000	61805	20526	17669	0	4403	57402	1379883	18203	162900	1177	239940	4744	952919
zr3644_18_R1_bismark_bt2_pe.bam	100000	62397	20763	16840	0	3891	58506	1400104	18495	162988	1162	242924	4926	969609
zr3644_19_R1_bismark_bt2_pe.bam	100000	61402	21445	17153	0	3620	57782	1391498	17611	160205	1159	239409	5021	968093
zr3644_1_R1_bismark_bt2_pe.bam	100000	62534	20244	17222	0	4122	58412	1373705	16457	160479	1093	238266	4561	952849
zr3644_20_R1_bismark_bt2_pe.bam	100000	61592	21962	16444	2	4189	57403	1402572	17549	162343	1151	241099	5152	975278
zr3644_21_R1_bismark_bt2_pe.bam	100000	61354	22075	16570	1	4196	57158	1396963	18229	160395	1108	240305	4713	972213
zr3644_22_R1_bismark_bt2_pe.bam	100000	61838	21374	16787	1	4048	57790	1400184	17967	162565	1195	241491	4901	972065
zr3644_23_R1_bismark_bt2_pe.bam	100000	61316	21132	17552	0	4107	57209	1354323	17488	157505	1183	233818	4909	939420
zr3644_24_R1_bismark_bt2_pe.bam	100000	62315	21022	16663	0	4182	58133	1405268	18046	163678	1163	242659	4781	974941
zr3644_2_R1_bismark_bt2_pe.bam	100000	61033	22427	16540	0	4139	56894	1418146	18079	163292	1195	242611	4889	988080
zr3644_3_R1_bismark_bt2_pe.bam	100000	61161	21806	17033	0	3670	57491	1386996	17858	160089	1119	237922	4720	965288
zr3644_4_R1_bismark_bt2_pe.bam	100000	61250	21911	16839	0	4161	57089	1371032	17454	155258	1054	232556	4473	960237
zr3644_5_R1_bismark_bt2_pe.bam	100000	61442	21828	16729	1	3845	57597	1398234	17568	159880	1182	239225	5075	975304
zr3644_6_R1_bismark_bt2_pe.bam	100000	61890	21393	16717	0	3916	57974	1393231	17907	159814	1145	237802	4957	971606
zr3644_7_R1_bismark_bt2_pe.bam	100000	60610	22770	16620	0	3499	57111	1384445	18084	158018	1133	236329	4741	966140
zr3644_8_R1_bismark_bt2_pe.bam	100000	61057	21754	17188	1	3698	57359	1371764	17946	158229	1112	236164	5133	953180
zr3644_9_R1_bismark_bt2_pe.bam	100000	61092	20677	18231	0	4373	56719	1283697	17534	147837	1072	221612	4784	890858
zrtg3616_1_R1_bismark_bt2_pe.bam	100000	62078	18843	19079	0	7811	54267	1111357	16063	135628	1008	198837	4642	755179
zrtg3616_2_R1_bismark_bt2_pe.bam	100000	61847	19291	18862	0	7757	54090	1094017	15537	133072	972	195204	4051	745181
zrtg3616_3_R1_bismark_bt2_pe.bam	100000	61506	18728	19766	0	7768	53738	999365	14715	119091	901	177915	3908	682835
zrtg3616_4_R1_bismark_bt2_pe.bam	100000	61653	18849	19498	0	7721	53932	1054411	15340	127416	965	189571	4152	716967
zrtg3616_5_R1_bismark_bt2_pe.bam	100000	61681	18693	19625	1	7372	54309	1037483	14188	125402	898	185487	4269	707239
zrtg3616_6_R1_bismark_bt2_pe.bam	100000	61511	18449	20040	0	8623	52888	978778	13835	118881	837	175160	3682	666383
zrtg3616_7_R1_bismark_bt2_pe.bam	100000	61554	19307	19138	1	7609	53945	1042333	15524	123948	930	184748	4069	713114
zrtg3616_8_R1_bismark_bt2_pe.bam	100000	61458	18881	19661	0	7466	53992	1057836	15560	128008	953	189631	4356	719328
zrtg3644_10_R1_bismark_bt2_pe.bam	100000	60926	22647	16426	1	3980	56946	1371132	18394	159797	1125	237123	4852	949841
zrtg3644_11_R1_bismark_bt2_pe.bam	100000	60730	22750	16520	0	4045	56685	1361369	17748	158161	1093	235802	4739	943826
zrtg3644_12_R1_bismark_bt2_pe.bam	100000	61267	22727	16006	0	3910	57357	1359316	16319	153209	1018	226939	4474	957357
zrtg3644_13_R1_bismark_bt2_pe.bam	100000	61532	22553	15915	0	4439	57093	1407110	18235	161556	1159	241902	4777	979481
zrtg3644_14_R1_bismark_bt2_pe.bam	100000	61818	22067	16114	1	4026	57792	1394909	20582	157518	1188	239212	4964	971445
zrtg3644_15_R1_bismark_bt2_pe.bam	100000	61239	22623	16138	0	3951	57288	1389611	19351	158139	1181	238682	4711	967547
zrtg3644_16_R1_bismark_bt2_pe.bam	100000	61417	21411	17172	0	4318	57099	1317943	17557	153340	1110	227936	4582	913418
zrtg3644_17_R1_bismark_bt2_pe.bam	100000	61619	21382	16999	0	4366	57253	1386305	18302	164021	1206	241401	4800	956575
zrtg3644_18_R1_bismark_bt2_pe.bam	100000	62205	21452	16343	0	3895	58310	1404454	18596	163930	1178	244043	4934	971773
zrtg3644_19_R1_bismark_bt2_pe.bam	100000	61076	22233	16691	0	3602	57474	1391794	17618	160667	1166	239818	4835	967690
zrtg3644_1_R1_bismark_bt2_pe.bam	100000	62198	21145	16657	0	4095	58103	1376985	16501	161661	1093	239101	4349	954280
zrtg3644_20_R1_bismark_bt2_pe.bam	100000	61432	22558	16008	2	4164	57268	1406127	17661	163291	1145	241742	4861	977427
zrtg3644_21_R1_bismark_bt2_pe.bam	100000	61032	22878	16090	0	4142	56890	1398119	18258	160954	1122	240595	4630	972560
zrtg3644_22_R1_bismark_bt2_pe.bam	100000	61648	22150	16201	1	4027	57621	1404024	18040	163600	1193	242229	4894	974068
zrtg3644_23_R1_bismark_bt2_pe.bam	100000	61099	21844	17057	0	4081	57018	1359016	17577	158275	1190	234950	4695	942329
zrtg3644_24_R1_bismark_bt2_pe.bam	100000	62084	21776	16140	0	4188	57896	1408564	18158	164256	1181	243584	4648	976737
zrtg3644_2_R1_bismark_bt2_pe.bam	100000	60791	23155	16054	0	4125	56666	1419476	18105	163850	1208	242924	5066	988323
zrtg3644_3_R1_bismark_bt2_pe.bam	100000	60870	22616	16514	0	3648	57222	1388599	17982	160404	1129	238481	4596	966007
zrtg3644_4_R1_bismark_bt2_pe.bam	100000	61001	22625	16374	0	4118	56883	1373862	17554	156232	1064	233363	4411	961238
zrtg3644_5_R1_bismark_bt2_pe.bam	100000	61139	22559	16302	0	3819	57320	1397855	17726	159944	1184	239762	4779	974460
zrtg3644_6_R1_bismark_bt2_pe.bam	100000	61547	22163	16290	0	3885	57662	1394445	18046	160195	1139	238321	4804	971940
zrtg3644_7_R1_bismark_bt2_pe.bam	100000	60320	23556	16124	0	3475	56845	1385784	18157	158602	1148	236768	4695	966414
zrtg3644_8_R1_bismark_bt2_pe.bam	100000	60857	22549	16593	1	3692	57165	1375616	18119	158953	1126	237093	5002	955323
zrtg3644_9_R1_bismark_bt2_pe.bam	100000	60757	21589	17654	0	4364	56393	1289022	17731	148754	1087	223139	4608	893703