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_R1_001_val_1_bismark_bt2_pe.bam	32105151	4636356	24877118	2591667	10	1228278	3408078	41089728	809455	3963864	90539	6906662	1196651	28122557
CF01-CM02-Larvae_R1_001_val_1_bismark_bt2_pe.bam	70708148	24971333	32368850	13367958	7	5928126	19043207	312429132	8731550	38345713	1186609	64329313	6444272	193391675
CF02-CM02-Zygote_R1_001_val_1_bismark_bt2_pe.bam	67063678	10105977	50657462	6300233	6	3151745	6954232	68800747	1494479	5899332	469414	10629429	4346748	45961345
CF03-CM03-Zygote_R1_001_val_1_bismark_bt2_pe.bam	64470157	16517061	38359026	9594063	7	4024267	12492794	150062562	3919996	14815997	698297	27156955	5713111	97758206
CF03-CM04-Larvae_R1_001_val_1_bismark_bt2_pe.bam	57667284	25130987	19755662	12780622	13	11215420	13915567	286520198	7059413	32490932	662641	56079819	3451337	186776056
CF03-CM05-Larvae_R1_001_val_1_bismark_bt2_pe.bam	48978052	17211016	23481673	8285361	2	3922817	13288199	249748547	7298824	29813254	1548651	50953449	6743014	153391355
CF04-CM04-Zygote_R1_001_val_1_bismark_bt2_pe.bam	41746657	10918276	25248177	5580199	5	2809948	8108328	115725833	2895514	11983878	514765	21345620	3459335	75526721
CF05-CM02-Larvae_R1_001_val_1_bismark_bt2_pe.bam	53936905	19268713	24852305	9815873	14	4841109	14427604	261975744	6990826	31782393	702897	53652034	3935709	164911885
CF05-CM05-Zygote_R1_001_val_1_bismark_bt2_pe.bam	73337225	19456469	43774341	10106407	8	4953870	14502599	215761875	6373641	23242439	1254343	41816798	7390530	135684124
CF06-CM01-Zygote_R1_001_val_1_bismark_bt2_pe.bam	82389335	21391006	49144786	11853536	7	5232408	16158598	194982120	5333947	19188766	1128807	34739930	8044239	126546431
CF06-CM02-Larvae_R1_001_val_1_bismark_bt2_pe.bam	49423309	11862382	31683507	5877412	8	2992167	8870215	136935257	4543213	13817899	1383099	25699283	7586137	83905626
CF07-CM02-Zygote_R1_001_val_1_bismark_bt2_pe.bam	60588756	7587675	48271147	4729927	7	2591171	4996504	64887224	1476446	6422420	210107	11624207	2571983	42582061
CF08-CM03-Zygote_R1_001_val_1_bismark_bt2_pe.bam	66096319	13081600	45148855	7865859	5	4113223	8968377	97330064	2079031	8634806	465841	15532345	4616696	66001345
CF08-CM04-Larvae_R1_001_val_1_bismark_bt2_pe.bam	54708068	1245366	52428088	1034614	0	560277	685089	8071590	126606	558446	39664	977524	1494281	4875069
CF08-CM05-Larvae_R1_001_val_1_bismark_bt2_pe.bam	63057346	1698854	60469188	889304	0	1408865	289989	5867837	95018	537095	18261	898809	373566	3945088
EF01-EM01-Zygote_R1_001_val_1_bismark_bt2_pe.bam	47718725	11837824	30005679	5875219	3	2928897	8908927	131551797	4206137	12856711	1155035	24410780	6414974	82508160
EF02-EM02-Zygote_R1_001_val_1_bismark_bt2_pe.bam	56944147	14177279	33479307	9287543	18	3371955	10805324	146553907	3242330	17384380	415358	28665884	3670331	93175624
EF03-EM03-Zygote_R1_001_val_1_bismark_bt2_pe.bam	132787654	24296251	94202406	14288991	6	7592724	16703527	190049367	4738667	17482361	1177474	32176756	8891401	125582708
EF03-EM04-Larvae_R1_001_val_1_bismark_bt2_pe.bam	74184423	23908326	38192824	12083263	10	6024420	17883906	295184891	9129077	31995225	2884396	57042151	12386503	181747539
EF03-EM05-Larvae_R1_001_val_1_bismark_bt2_pe.bam	57495743	17368215	31935230	8192290	8	3913288	13454927	236950745	6893130	26834706	1561244	46665845	7228228	147767592
EF04-EM04-Zygote_R1_001_val_1_bismark_bt2_pe.bam	70141415	9554872	54144932	6441587	24	2671957	6882915	67957021	1546006	7085137	497366	11636302	3097887	44094323
EF04-EM05-Larvae_R1_001_val_1_bismark_bt2_pe.bam	45628766	16508152	21474728	7645881	5	4293073	12215079	245132023	6318934	29453595	647341	49546217	3224958	155940978
EF05-EM01-Larvae_R1_001_val_1_bismark_bt2_pe.bam	39294742	11922545	21460435	5911759	3	3088153	8834392	166834306	4617923	20109284	519586	34301616	3068644	104217253
EF05-EM05-Zygote_R1_001_val_1_bismark_bt2_pe.bam	48548054	4410412	40594655	3542980	7	1211340	3199072	28591365	433213	2905613	84371	4576987	1439414	19151767
EF05-EM06-Larvae_R1_001_val_1_bismark_bt2_pe.bam	62575164	21714864	32866900	7993392	8	8254904	13459960	333355883	8758572	35840966	2939623	59986409	12862135	212968178
EF06-EM01-Larvae_R1_001_val_1_bismark_bt2_pe.bam	56782240	19254172	28725008	8803047	13	4503581	14750591	299708571	7531004	35161182	886898	58901598	4401630	192826259
EF06-EM02-Larvae_R1_001_val_1_bismark_bt2_pe.bam	53188835	19330841	24520436	9337551	7	4897465	14433376	254099662	7737892	29947094	1276886	52390291	5710580	157036919
EF06-EM06-Larvae_R1_001_val_1_bismark_bt2_pe.bam	80247899	21726829	48022455	10498595	20	13588458	8138371	119766527	2938477	11487595	820919	20543897	4945042	79030597
EF07-EM01-Zygote_R1_001_val_1_bismark_bt2_pe.bam	75480641	8248828	61730915	5500889	9	3271370	4977458	57038120	1055701	5660416	122873	9636803	1904204	38658123
EF07-EM03-Larvae_R1_001_val_1_bismark_bt2_pe.bam	48379049	15618584	25139522	7620937	6	4213349	11405235	217099541	5580527	24851645	650121	43074617	3495169	139447462
EF08-EM03-Larvae_R1_001_val_1_bismark_bt2_pe.bam	50784782	18568098	21834010	10382671	3	6067005	12501093	226007355	6138664	26636206	503168	45933567	3098933	143696817
EF08-EM04-Larvae_R1_001_val_1_bismark_bt2_pe.bam	62743331	22325555	27547702	12870053	21	5521180	16804375	262376593	7910157	31080214	1257384	54129192	6578903	161420743