Methyl-MiniSeq Analysis Report for in0007

General Statistics

Showing ⁸³/₁₆₆ rows and ⁶/₂₃ columns.

Sample Name	% Dups	% GC	Length	% Failed	Seqs	# Reads	% BP Trimmed	% Dups	% GC	Length	% Failed	Seqs	# Reads	Aligned	% Uniquely Aligned	% BS Conversion (Non-CpG)	Insert Size	Mean Insert Size	Aligned	% Uniquely Aligned	% BS Conversion (Spike-in)	Uniq. CpG	Avg. CpG Coverage
in3670_13	70.6%	39%	151 bp	27%	27940127	27940127	33.7%	66.6%	28%	97 bp	18%	27893464	27893464	14429984	51.7%	98.1%	89 bp	108 bp	119016	0.4%	98.5%	7736919	6X
in3670_13_R2	68.7%	38%	151 bp	36%	27940127		33.6%	65.2%	29%	98 bp	36%	27893464
in3670_14	74.3%	35%	151 bp	27%	45160784	45160784	25.6%	71.2%	28%	110 bp	18%	45115049	45115049	25342848	56.2%	98.5%	124 bp	129 bp	199128	0.4%	99.0%	8929145	10X
in3670_14_R2	72.6%	35%	151 bp	36%	45160784		25.2%	69.8%	29%	110 bp	36%	45115049
in3670_15	66.0%	37%	151 bp	27%	23799255	23799255	29.1%	62.5%	28%	105 bp	18%	23776646	23776646	13538879	56.9%	98.7%	120 bp	119 bp	158654	0.7%	99.0%	8099869	6X
in3670_15_R2	64.0%	37%	151 bp	36%	23799255		28.6%	60.7%	29%	105 bp	36%	23776646
in3670_16	73.4%	37%	151 bp	27%	41229206	41229206	29.8%	70.0%	28%	104 bp	18%	41175851	41175851	23243168	56.4%	98.8%	107 bp	123 bp	117153	0.3%	99.1%	9125299	9X
in3670_16_R2	71.8%	36%	151 bp	36%	41229206		29.2%	69.0%	29%	104 bp	36%	41175851
in3670_17	72.6%	36%	151 bp	27%	37930088	37930088	27.3%	69.7%	27%	107 bp	18%	37881422	37881422	21676743	57.2%	98.9%	125 bp	128 bp	144703	0.4%	99.2%	9007364	9X
in3670_17_R2	70.8%	36%	151 bp	36%	37930088		26.7%	68.1%	29%	108 bp	36%	37881422
in3670_18	72.8%	35%	151 bp	27%	40856257	40856257	26.1%	69.7%	28%	109 bp	18%	40810471	40810471	24126732	59.1%	99.0%	127 bp	132 bp	131999	0.3%	99.3%	9189420	10X
in3670_18_R2	72.0%	35%	151 bp	36%	40856257		25.6%	69.2%	29%	110 bp	36%	40810471
zr9490_109	68.7%	36%	151 bp	27%	44829490	44829490	26.3%	64.8%	28%	109 bp	18%	44748716	44748716	24878527	55.6%	98.6%	123 bp	129 bp	128173	0.3%	99.2%	10168079	9X
zr9490_109_R2	65.5%	36%	151 bp	36%	44829490		25.7%	62.2%	29%	110 bp	27%	44748716
zr9490_119	65.6%	39%	151 bp	27%	28627628	28627628	29.6%	61.9%	30%	104 bp	18%	28533233	28533233	12751431	44.7%	97.7%	99 bp	117 bp	88465	0.3%	98.8%	7963729	6X
zr9490_119_R2	62.5%	37%	151 bp	36%	28627628		28.8%	59.6%	31%	105 bp	18%	28533233
zr9490_17	69.9%	37%	151 bp	27%	40012243	40012243	26.7%	66.4%	29%	108 bp	18%	39904922	39904922	21044464	52.7%	98.2%	127 bp	129 bp	157627	0.4%	99.0%	8998817	8X
zr9490_17_R2	67.6%	37%	151 bp	36%	40012243		26.2%	64.6%	30%	109 bp	18%	39904922
zr9490_181	63.3%	37%	151 bp	27%	35232941	35232941	26.3%	59.9%	29%	109 bp	18%	35131238	35131238	12651676	36.0%	98.5%	114 bp	126 bp	226599	0.6%	99.2%	8789765	5X
zr9490_181_R2	59.6%	37%	151 bp	36%	35232941		25.6%	56.8%	30%	110 bp	27%	35131238
zr9490_182	66.2%	36%	151 bp	27%	45472150	45472150	26.6%	62.0%	29%	108 bp	18%	45371251	45371251	22577976	49.8%	98.5%	124 bp	130 bp	164948	0.4%	99.1%	9911348	8X
zr9490_182_R2	63.3%	36%	151 bp	36%	45472150		26.1%	59.8%	30%	109 bp	27%	45371251
zr9490_183	59.8%	36%	151 bp	27%	29638416	29638416	23.9%	55.9%	29%	112 bp	18%	29574125	29574125	15551360	52.6%	98.5%	131 bp	134 bp	144919	0.5%	99.1%	9352016	6X
zr9490_183_R2	57.6%	36%	151 bp	36%	29638416		23.5%	54.3%	30%	113 bp	36%	29574125
zr9490_184	69.2%	37%	151 bp	27%	48206799	48206799	27.9%	65.6%	29%	106 bp	18%	48100084	48100084	24204453	50.3%	98.0%	129 bp	127 bp	251665	0.5%	99.1%	9691237	9X
zr9490_184_R2	67.1%	36%	151 bp	36%	48206799		27.4%	64.1%	30%	107 bp	27%	48100084
zr9490_185	65.0%	37%	151 bp	27%	34638960	34638960	26.5%	61.1%	29%	108 bp	18%	34557078	34557078	16444634	47.6%	98.0%	120 bp	128 bp	119901	0.3%	98.8%	8991393	6X
zr9490_185_R2	61.6%	36%	151 bp	36%	34638960		26.0%	58.3%	30%	109 bp	18%	34557078
zr9490_187	69.1%	37%	151 bp	27%	46154329	46154329	27.7%	65.2%	29%	107 bp	18%	46051225	46051225	23664491	51.4%	98.5%	116 bp	127 bp	180195	0.4%	99.1%	9518474	9X
zr9490_187_R2	66.1%	37%	151 bp	36%	46154329		27.1%	62.8%	30%	107 bp	27%	46051225
zr9490_189	64.6%	38%	151 bp	27%	28299510	28299510	27.8%	60.7%	29%	106 bp	18%	28226012	28226012	11469797	40.6%	97.7%	104 bp	121 bp	113828	0.4%	98.8%	7627226	5X
zr9490_189_R2	62.2%	37%	151 bp	36%	28299510		27.5%	59.0%	30%	107 bp	18%	28226012
zr9490_19	65.5%	37%	151 bp	27%	30116306	30116306	24.7%	61.9%	29%	111 bp	18%	30036703	30036703	16056397	53.5%	98.2%	134 bp	134 bp	120615	0.4%	98.9%	8760665	7X
zr9490_190	65.6%	38%	151 bp	27%	31752348	31752348	28.7%	61.8%	29%	105 bp	18%	31639292	31639292	11394049	36.0%	97.7%	101 bp	120 bp	111630	0.4%	98.8%	7364388	5X
zr9490_190_R2	62.2%	37%	151 bp	36%	31752348		28.1%	59.3%	30%	106 bp	27%	31639292
zr9490_191	59.6%	37%	151 bp	27%	22561525	22561525	27.8%	55.3%	29%	106 bp	18%	22499221	22499221	10658777	47.4%	98.0%	111 bp	123 bp	100965	0.4%	98.9%	8016635	5X
zr9490_191_R2	56.5%	38%	151 bp	36%	22561525		27.3%	52.8%	30%	107 bp	18%	22499221
zr9490_192	64.4%	38%	151 bp	27%	26255165	26255165	27.7%	60.5%	30%	107 bp	18%	26184469	26184469	12388911	47.3%	98.2%	115 bp	122 bp	155635	0.6%	99.1%	7891596	6X
zr9490_192_R2	61.8%	36%	151 bp	36%	26255165		27.1%	58.7%	30%	107 bp	27%	26184469
zr9490_193	69.5%	38%	151 bp	27%	36876177	36876177	27.9%	65.7%	30%	106 bp	18%	36758946	36758946	17583725	47.8%	98.5%	107 bp	124 bp	144823	0.4%	99.2%	8536367	8X
zr9490_193_R2	66.3%	37%	151 bp	36%	36876177		27.2%	63.4%	31%	107 bp	27%	36758946
zr9490_194	68.1%	38%	151 bp	27%	27926970	27926970	26.4%	64.5%	30%	109 bp	18%	27829230	27829230	11928894	42.9%	97.8%	125 bp	126 bp	139694	0.5%	98.9%	7460537	6X
zr9490_194_R2	65.4%	38%	151 bp	36%	27926970		25.7%	62.6%	31%	109 bp	36%	27829230
zr9490_195	64.7%	37%	151 bp	27%	29860873	29860873	25.3%	60.8%	30%	110 bp	18%	29775774	29775774	14615255	49.1%	98.5%	126 bp	132 bp	118459	0.4%	99.1%	8830901	6X
zr9490_195_R2	60.9%	37%	151 bp	36%	29860873		24.7%	57.8%	31%	111 bp	27%	29775774
zr9490_196	63.1%	40%	151 bp	27%	27146310	27146310	29.0%	59.0%	30%	104 bp	18%	27075947	27075947	13304479	49.1%	98.1%	101 bp	116 bp	139846	0.5%	99.0%	8539247	5X
zr9490_196_R2	57.6%	37%	151 bp	36%	27146310		28.8%	54.2%	31%	105 bp	18%	27075947
zr9490_197	68.3%	38%	151 bp	27%	37299060	37299060	32.0%	64.2%	30%	100 bp	18%	37168139	37168139	14536966	39.1%	97.3%	89 bp	108 bp	125637	0.3%	98.7%	7681186	6X
zr9490_197_R2	65.7%	38%	151 bp	36%	37299060		31.4%	62.4%	31%	101 bp	27%	37168139
zr9490_198	57.5%	39%	151 bp	27%	17773555	17773555	28.2%	53.5%	29%	105 bp	18%	17712466	17712466	6719699	37.9%	97.5%	101 bp	118 bp	69623	0.4%	98.6%	6654879	3X
zr9490_198_R2	54.0%	38%	151 bp	36%	17773555		27.8%	50.7%	30%	106 bp	27%	17712466
zr9490_199	67.8%	38%	151 bp	27%	36435699	36435699	28.3%	64.0%	30%	106 bp	18%	36319999	36319999	17196471	47.3%	98.2%	104 bp	119 bp	156387	0.4%	99.1%	8647956	7X
zr9490_199_R2	63.9%	37%	151 bp	36%	36435699		27.6%	60.7%	31%	107 bp	27%	36319999
zr9490_19_R2	62.6%	36%	151 bp	36%	30116306		24.2%	59.6%	30%	112 bp	18%	30036703
zr9490_200	64.6%	39%	151 bp	27%	21954839	21954839	26.6%	60.9%	30%	108 bp	18%	21876838	21876838	10000441	45.7%	97.1%	114 bp	121 bp	115312	0.5%	98.7%	7303928	5X
zr9490_200_R2	61.3%	38%	151 bp	36%	21954839		26.0%	58.4%	31%	109 bp	36%	21876838
zr9490_201	69.8%	37%	151 bp	27%	45666739	45666739	25.9%	66.6%	30%	109 bp	18%	45513341	45513341	22259229	48.9%	98.2%	115 bp	125 bp	249697	0.5%	99.2%	9681610	8X
zr9490_201_R2	66.1%	37%	151 bp	36%	45666739		25.3%	63.7%	31%	110 bp	27%	45513341
zr9490_202	64.2%	38%	151 bp	27%	26255255	26255255	27.7%	60.5%	30%	107 bp	18%	26155017	26155017	11037899	42.2%	98.0%	104 bp	120 bp	144639	0.6%	99.0%	7825593	5X
zr9490_202_R2	60.8%	37%	151 bp	36%	26255255		27.0%	57.9%	31%	107 bp	27%	26155017
zr9490_203	62.0%	37%	151 bp	27%	36624408	36624408	27.0%	58.1%	29%	108 bp	18%	36519052	36519052	18429835	50.5%	98.1%	113 bp	126 bp	206670	0.6%	99.2%	10353211	7X
zr9490_203_R2	59.1%	38%	151 bp	36%	36624408		26.3%	56.0%	31%	109 bp	27%	36519052
zr9490_204	65.6%	37%	151 bp	27%	36710427	36710427	24.7%	62.2%	29%	111 bp	18%	36607748	36607748	19836827	54.2%	98.5%	132 bp	132 bp	227404	0.6%	99.3%	10073595	7X
zr9490_204_R2	62.6%	36%	151 bp	36%	36710427		24.1%	59.8%	30%	112 bp	27%	36607748
zr9490_205	66.8%	37%	151 bp	27%	35201348	35201348	30.9%	62.2%	29%	102 bp	18%	35120296	35120296	16091674	45.8%	97.4%	94 bp	114 bp	88580	0.3%	98.5%	8501543	6X
zr9490_205_R2	64.1%	39%	151 bp	36%	35201348		30.2%	60.3%	30%	103 bp	27%	35120296
zr9490_206	66.8%	38%	151 bp	27%	29334826	29334826	28.8%	62.7%	29%	105 bp	18%	29257811	29257811	15670356	53.6%	97.9%	108 bp	120 bp	111525	0.4%	98.7%	8319529	6X
zr9490_206_R2	64.3%	36%	151 bp	36%	29334826		28.3%	61.0%	30%	106 bp	27%	29257811
zr9490_25	70.5%	36%	151 bp	27%	44833355	44833355	25.7%	67.3%	29%	110 bp	18%	44706692	44706692	23099933	51.7%	98.3%	129 bp	128 bp	247478	0.6%	99.1%	8825923	10X
zr9490_25_R2	68.5%	36%	151 bp	36%	44833355		25.1%	65.9%	30%	110 bp	27%	44706692
zr9490_26	66.7%	36%	151 bp	27%	31905387	31905387	25.3%	63.1%	29%	110 bp	18%	31812059	31812059	16918613	53.2%	98.2%	128 bp	133 bp	113715	0.4%	98.9%	8687467	7X
zr9490_26_R2	64.3%	37%	151 bp	36%	31905387		24.8%	61.4%	30%	111 bp	27%	31812059
zr9490_3	70.7%	36%	151 bp	27%	46898917	46898917	24.5%	67.6%	28%	111 bp	18%	46783419	46783419	25169623	53.8%	98.5%	135 bp	133 bp	287397	0.6%	99.1%	9388066	10X
zr9490_32	71.2%	38%	151 bp	27%	34935921	34935921	26.3%	67.6%	29%	108 bp	18%	34818785	34818785	16903549	48.5%	96.4%	120 bp	125 bp	120568	0.3%	97.9%	7754663	7X
zr9490_32_R2	69.2%	36%	151 bp	36%	34935921		26.3%	66.4%	30%	109 bp	27%	34818785
zr9490_33	68.2%	37%	151 bp	27%	33843155	33843155	25.6%	64.6%	29%	110 bp	18%	33749092	33749092	17301250	51.3%	98.3%	128 bp	133 bp	101880	0.3%	99.0%	8698734	7X
zr9490_33_R2	66.1%	36%	151 bp	36%	33843155		25.2%	63.3%	29%	110 bp	27%	33749092
zr9490_34	71.0%	37%	151 bp	27%	41796565	41796565	27.8%	67.3%	28%	106 bp	18%	41698347	41698347	21380202	51.3%	98.0%	123 bp	127 bp	171903	0.4%	98.9%	8919200	8X
zr9490_34_R2	68.7%	37%	151 bp	36%	41796565		27.3%	65.7%	29%	107 bp	18%	41698347
zr9490_35	70.7%	36%	151 bp	27%	35092914	35092914	25.9%	67.2%	28%	109 bp	18%	34982623	34982623	17480443	50.0%	96.9%	123 bp	131 bp	77727	0.2%	98.4%	8219675	7X
zr9490_35_R2	68.2%	36%	151 bp	36%	35092914		25.6%	65.3%	29%	110 bp	18%	34982623
zr9490_36	69.7%	38%	151 bp	27%	29701702	29701702	26.7%	66.0%	28%	108 bp	18%	29613807	29613807	14235407	48.1%	96.2%	123 bp	129 bp	78607	0.3%	98.0%	7650640	6X
zr9490_36_R2	67.7%	36%	151 bp	36%	29701702		26.5%	64.8%	29%	108 bp	27%	29613807
zr9490_3_R2	67.9%	36%	151 bp	36%	46898917		24.0%	65.5%	29%	112 bp	27%	46783419
zr9490_4	68.2%	36%	151 bp	27%	35418772	35418772	24.6%	64.8%	29%	111 bp	18%	35311560	35311560	16890644	47.8%	98.1%	127 bp	133 bp	111329	0.3%	99.0%	8566605	7X
zr9490_41	70.3%	38%	151 bp	27%	37290770	37290770	26.2%	66.5%	29%	108 bp	18%	37188578	37188578	19081315	51.3%	97.9%	118 bp	126 bp	109758	0.3%	98.9%	8404216	8X
zr9490_41_R2	67.7%	36%	151 bp	36%	37290770		26.2%	64.6%	30%	109 bp	18%	37188578
zr9490_43	71.9%	37%	151 bp	27%	43898239	43898239	24.7%	68.4%	29%	111 bp	18%	43773855	43773855	24142030	55.2%	98.5%	133 bp	134 bp	232728	0.5%	99.1%	9177277	10X
zr9490_43_R2	69.6%	36%	151 bp	36%	43898239		24.2%	66.9%	30%	112 bp	36%	43773855
zr9490_46	68.2%	38%	151 bp	27%	28939869	28939869	28.5%	64.5%	28%	106 bp	18%	28856110	28856110	14343467	49.7%	97.7%	114 bp	123 bp	105528	0.4%	98.6%	8070402	6X
zr9490_46_R2	64.6%	36%	151 bp	36%	28939869		27.8%	61.6%	29%	106 bp	27%	28856110
zr9490_47	69.9%	37%	151 bp	27%	38564769	38564769	28.0%	66.1%	29%	106 bp	18%	38470132	38470132	20337355	52.9%	97.7%	115 bp	122 bp	169613	0.4%	98.5%	8718273	8X
zr9490_47_R2	66.2%	37%	151 bp	36%	38564769		27.7%	63.1%	30%	106 bp	27%	38470132
zr9490_48	68.9%	37%	151 bp	27%	33025337	33025337	27.5%	65.2%	29%	107 bp	18%	32944626	32944626	17162326	52.1%	97.9%	116 bp	125 bp	119341	0.4%	98.8%	8532454	7X
zr9490_48_R2	64.5%	37%	151 bp	36%	33025337		26.9%	61.4%	30%	108 bp	18%	32944626
zr9490_49	69.3%	38%	151 bp	27%	35063225	35063225	29.0%	65.4%	29%	105 bp	18%	34970884	34970884	17676394	50.5%	97.2%	110 bp	119 bp	150136	0.4%	98.3%	8139626	7X
zr9490_49_R2	67.4%	37%	151 bp	36%	35063225		28.5%	64.3%	30%	105 bp	27%	34970884
zr9490_4_R2	65.6%	36%	151 bp	36%	35418772		24.1%	63.0%	30%	112 bp	27%	35311560
zr9490_50	68.6%	40%	151 bp	27%	27269567	27269567	34.8%	64.2%	29%	96 bp	18%	27193722	27193722	12699516	46.7%	96.3%	88 bp	107 bp	64089	0.2%	97.7%	7154498	6X
zr9490_50_R2	66.3%	38%	151 bp	36%	27269567		34.1%	62.8%	30%	97 bp	18%	27193722
zr9490_51	69.9%	38%	151 bp	27%	34498573	34498573	31.3%	65.9%	29%	101 bp	18%	34402090	34402090	16566948	48.2%	96.7%	98 bp	115 bp	115585	0.3%	98.1%	7863847	7X
zr9490_51_R2	67.1%	38%	151 bp	36%	34498573		30.7%	63.8%	30%	102 bp	27%	34402090
zr9490_52	71.0%	37%	151 bp	27%	46047835	46047835	27.0%	67.4%	28%	108 bp	18%	45930175	45930175	23118271	50.3%	97.6%	122 bp	127 bp	175142	0.4%	98.7%	8987786	9X
zr9490_52_R2	68.6%	36%	151 bp	36%	46047835		26.5%	65.6%	29%	108 bp	27%	45930175
zr9490_53	68.2%	38%	151 bp	27%	33360453	33360453	29.8%	64.3%	29%	103 bp	18%	33271898	33271898	16121755	48.5%	97.1%	109 bp	118 bp	142658	0.4%	98.4%	8110565	7X
zr9490_53_R2	65.9%	38%	151 bp	36%	33360453		29.2%	62.9%	30%	104 bp	27%	33271898
zr9490_54	68.3%	37%	151 bp	27%	36514003	36514003	27.4%	64.4%	29%	107 bp	18%	36418751	36418751	17874630	49.1%	97.6%	114 bp	126 bp	122373	0.3%	98.7%	8611393	7X
zr9490_54_R2	64.7%	36%	151 bp	36%	36514003		26.8%	61.6%	30%	108 bp	27%	36418751
zr9490_55	67.1%	37%	151 bp	27%	32042295	32042295	28.7%	63.2%	28%	105 bp	18%	31960255	31960255	16592739	51.9%	98.0%	115 bp	122 bp	155286	0.5%	98.8%	8586037	7X
zr9490_55_R2	64.6%	37%	151 bp	36%	32042295		28.2%	61.4%	29%	106 bp	27%	31960255
zr9490_56	72.2%	40%	151 bp	27%	38112367	38112367	36.8%	67.9%	30%	93 bp	18%	38006735	38006735	18194478	47.9%	95.7%	81 bp	100 bp	77516	0.2%	97.4%	7385122	8X
zr9490_56_R2	68.9%	40%	151 bp	36%	38112367		35.8%	65.3%	31%	94 bp	27%	38006735
zr9490_58	71.5%	37%	151 bp	27%	46045149	46045149	31.0%	67.6%	29%	102 bp	18%	45922578	45922578	22617779	49.3%	96.9%	98 bp	119 bp	106454	0.2%	98.3%	8862945	9X
zr9490_58_R2	69.3%	37%	151 bp	36%	46045149		30.4%	66.1%	30%	102 bp	18%	45922578
zr9490_59	68.3%	41%	151 bp	27%	28180488	28180488	36.1%	63.8%	29%	94 bp	18%	28093283	28093283	13189140	46.9%	94.9%	85 bp	106 bp	43457	0.2%	96.7%	7342783	6X
zr9490_59_R2	65.5%	40%	151 bp	36%	28180488		35.3%	61.7%	31%	95 bp	27%	28093283
zr9490_60	68.4%	37%	151 bp	27%	41120265	41120265	29.9%	64.4%	29%	103 bp	18%	41032390	41032390	22341201	54.4%	98.1%	108 bp	120 bp	161290	0.4%	98.9%	9452002	8X
zr9490_60_R2	66.4%	36%	151 bp	36%	41120265		29.4%	63.1%	30%	104 bp	18%	41032390
zr9490_61	66.1%	40%	151 bp	27%	28866441	28866441	32.1%	62.3%	29%	100 bp	18%	28791540	28791540	13942845	48.4%	97.0%	101 bp	113 bp	122771	0.4%	98.1%	7952845	6X
zr9490_61_R2	63.4%	39%	151 bp	36%	28866441		31.4%	60.2%	30%	101 bp	27%	28791540
zr9490_62	70.4%	38%	151 bp	27%	34407610	34407610	30.1%	66.5%	29%	103 bp	18%	34309022	34309022	16788158	48.9%	97.2%	99 bp	116 bp	96903	0.3%	98.5%	7958796	7X
zr9490_62_R2	66.7%	37%	151 bp	36%	34407610		29.5%	63.6%	30%	104 bp	27%	34309022
zr9490_63	71.2%	37%	151 bp	27%	43393390	43393390	27.7%	67.3%	29%	106 bp	18%	43280361	43280361	23768362	54.9%	97.9%	120 bp	129 bp	122835	0.3%	98.8%	9307361	9X
zr9490_63_R2	68.8%	36%	151 bp	36%	43393390		27.2%	65.7%	30%	107 bp	18%	43280361
zr9490_64	67.9%	37%	151 bp	27%	30599325	30599325	26.4%	64.1%	29%	108 bp	18%	30517148	30517148	16788886	55.0%	97.9%	128 bp	131 bp	104280	0.3%	98.8%	8649741	7X
zr9490_64_R2	65.4%	37%	151 bp	36%	30599325		26.0%	62.1%	30%	109 bp	27%	30517148
zr9490_65	71.1%	37%	151 bp	27%	44501412	44501412	28.4%	67.6%	29%	106 bp	18%	44381132	44381132	23943079	53.9%	98.6%	121 bp	124 bp	242479	0.5%	99.2%	9357482	10X
zr9490_65_R2	68.9%	37%	151 bp	36%	44501412		27.8%	66.1%	30%	106 bp	18%	44381132
zr9490_68	69.8%	37%	151 bp	27%	40519438	40519438	28.1%	66.2%	29%	106 bp	18%	40407282	40407282	20787650	51.4%	98.1%	127 bp	126 bp	222980	0.6%	98.9%	8794769	8X
zr9490_68_R2	67.7%	37%	151 bp	36%	40519438		27.4%	65.0%	30%	107 bp	27%	40407282
zr9490_69	69.1%	38%	151 bp	27%	37338070	37338070	27.7%	65.8%	29%	106 bp	18%	37231793	37231793	20246990	54.4%	98.5%	130 bp	126 bp	234342	0.6%	99.1%	8900869	8X
zr9490_69_R2	65.8%	36%	151 bp	36%	37338070		27.1%	63.1%	30%	107 bp	27%	37231793
zr9490_73	73.0%	40%	151 bp	27%	35713998	35713998	36.0%	68.6%	30%	94 bp	18%	35606709	35606709	17051664	47.9%	97.1%	82 bp	105 bp	68184	0.2%	98.5%	7403691	7X
zr9490_73_R2	71.0%	39%	151 bp	36%	35713998		35.2%	67.6%	31%	95 bp	27%	35606709
zr9490_74	71.3%	38%	151 bp	27%	35408827	35408827	30.8%	67.2%	29%	102 bp	18%	35315754	35315754	17465023	49.5%	97.1%	100 bp	116 bp	104004	0.3%	98.3%	7915082	7X
zr9490_74_R2	68.9%	38%	151 bp	36%	35408827		30.3%	65.7%	30%	103 bp	18%	35315754
zr9490_75	69.4%	38%	151 bp	27%	35371962	35371962	28.1%	65.8%	28%	106 bp	18%	35279003	35279003	18688400	53.0%	97.9%	125 bp	122 bp	180997	0.5%	98.8%	8698793	7X
zr9490_75_R2	66.8%	37%	151 bp	36%	35371962		27.5%	63.9%	30%	107 bp	27%	35279003
zr9490_76	67.8%	36%	151 bp	27%	34435008	34435008	22.9%	64.2%	28%	114 bp	18%	34355946	34355946	19128480	55.7%	98.5%	146 bp	141 bp	107301	0.3%	99.2%	9031732	8X
zr9490_76_R2	65.4%	35%	151 bp	36%	34435008		22.5%	62.4%	29%	114 bp	27%	34355946
zr9490_77	71.3%	36%	151 bp	27%	44616542	44616542	26.3%	67.5%	28%	109 bp	18%	44502551	44502551	23516448	52.8%	98.0%	126 bp	128 bp	172340	0.4%	98.9%	8834449	9X
zr9490_77_R2	69.0%	36%	151 bp	36%	44616542		25.8%	65.9%	29%	109 bp	36%	44502551
zr9490_79	67.9%	37%	151 bp	27%	37928926	37928926	23.7%	64.6%	28%	112 bp	18%	37832959	37832959	21264992	56.2%	98.4%	138 bp	133 bp	233188	0.6%	99.1%	9177146	8X
zr9490_79_R2	65.7%	36%	151 bp	36%	37928926		23.7%	63.0%	29%	112 bp	27%	37832959
zr9490_80	73.5%	39%	151 bp	27%	42346758	42346758	33.2%	69.6%	29%	98 bp	18%	42210037	42210037	20694685	49.0%	96.6%	91 bp	109 bp	118199	0.3%	98.0%	7996354	8X
zr9490_80_R2	70.9%	37%	151 bp	36%	42346758		32.5%	67.7%	30%	99 bp	18%	42210037
zr9490_81	66.0%	41%	151 bp	27%	17801405	17801405	32.2%	61.8%	29%	99 bp	18%	17739627	17739627	8665127	48.8%	96.4%	91 bp	109 bp	57244	0.3%	97.6%	6477379	4X
zr9490_81_R2	62.5%	39%	151 bp	36%	17801405		32.1%	59.0%	31%	100 bp	27%	17739627
zr9490_82	71.8%	37%	151 bp	27%	46064190	46064190	28.0%	68.4%	28%	106 bp	18%	45911162	45911162	23241832	50.6%	97.6%	123 bp	126 bp	232895	0.5%	98.7%	8952878	9X
zr9490_82_R2	68.7%	36%	151 bp	36%	46064190		27.3%	66.0%	29%	107 bp	27%	45911162
zr9490_83	63.9%	38%	151 bp	27%	32657176	32657176	29.4%	60.1%	28%	104 bp	18%	32571575	32571575	15459530	47.5%	97.5%	113 bp	118 bp	150445	0.5%	98.6%	8752405	6X
zr9490_83_R2	61.2%	38%	151 bp	36%	32657176		28.9%	58.1%	29%	105 bp	27%	32571575
zr9490_84	68.6%	38%	151 bp	27%	28391061	28391061	27.6%	64.8%	29%	106 bp	18%	28310276	28310276	14686869	51.9%	97.8%	112 bp	124 bp	77954	0.3%	98.7%	8072856	6X
zr9490_84_R2	65.4%	37%	151 bp	36%	28391061		27.3%	62.4%	30%	107 bp	18%	28310276
zr9490_85	69.9%	38%	151 bp	27%	35979956	35979956	32.2%	65.8%	29%	100 bp	18%	35867219	35867219	17889686	49.9%	97.4%	96 bp	112 bp	114759	0.3%	98.5%	8327135	7X
zr9490_85_R2	67.1%	38%	151 bp	36%	35979956		31.6%	63.7%	30%	101 bp	27%	35867219
zr9490_86	63.3%	37%	151 bp	27%	21830653	21830653	25.5%	59.3%	29%	110 bp	18%	21767883	21767883	10991666	50.5%	98.5%	125 bp	129 bp	96329	0.4%	99.1%	7758517	6X
zr9490_86_R2	60.3%	36%	151 bp	36%	21830653		25.4%	57.3%	30%	110 bp	27%	21767883
zr9490_87	67.9%	36%	151 bp	27%	37684161	37684161	25.8%	64.3%	28%	110 bp	18%	37587348	37587348	19917482	53.0%	98.3%	129 bp	126 bp	226974	0.6%	98.9%	8744798	8X
zr9490_87_R2	64.8%	36%	151 bp	36%	37684161		25.2%	61.8%	29%	110 bp	27%	37587348
zr9490_88	67.4%	36%	151 bp	27%	43176735	43176735	24.9%	63.6%	28%	111 bp	18%	43067065	43067065	23532725	54.6%	98.7%	133 bp	137 bp	179796	0.4%	99.2%	9942176	9X
zr9490_88_R2	64.9%	35%	151 bp	36%	43176735		24.4%	61.9%	29%	111 bp	18%	43067065
zr9490_89	64.7%	36%	151 bp	27%	39722952	39722952	23.2%	61.0%	28%	113 bp	18%	39629282	39629282	23090972	58.3%	98.7%	141 bp	138 bp	133178	0.3%	99.2%	11212252	7X
zr9490_89_R2	61.0%	35%	151 bp	36%	39722952		22.6%	57.9%	29%	114 bp	27%	39629282
zr9490_90	64.9%	36%	151 bp	27%	41696278	41696278	24.1%	61.3%	28%	112 bp	18%	41607168	41607168	24125161	58.0%	98.7%	138 bp	137 bp	154350	0.4%	99.2%	11178896	8X
zr9490_90_R2	62.7%	35%	151 bp	36%	41696278		23.6%	59.6%	29%	113 bp	18%	41607168

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	FastQC (raw)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (raw)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (raw)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (raw)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (raw)	Seqs	Total Sequences (units)	`total_sequences`	read_count
\|\|	FastQC (raw)	# Reads	Total Reads (units)	`sequences_in_total`	read_count
\|\|	Cutadapt	% BP Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None
\|\|	FastQC (trimmed)	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	FastQC (trimmed)	% GC	Average % GC Content	`percent_gc`	None
\|\|	FastQC (trimmed)	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	FastQC (trimmed)	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	FastQC (trimmed)	Seqs	Total Sequences (units)	`total_sequences`	read_count
\|\|	FastQC (trimmed)	# Reads	Total Reads (units)	`sequences_in_total`	read_count
\|\|	Bismark	Aligned	Total Aligned Sequences (units)	`aligned_reads`	read_count
\|\|	Bismark	% Uniquely Aligned	Percent Aligned Sequences	`percent_aligned`	None
\|\|	Bismark	% BS Conversion (Non-CpG)	Percent Bisulfite Conversion Rate	`percent_bs_conversion`	None
\|\|	Insert Size	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	Insert Size	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None
\|\|	Bismark (spike-in)	Aligned	Total Aligned Sequences (units)	`aligned_reads`	read_count
\|\|	Bismark (spike-in)	% Uniquely Aligned	Percent Aligned Sequences	`percent_aligned`	None
\|\|	Bismark (spike-in)	% BS Conversion (Spike-in)	Percent Bisulfite Conversion Rate	`percent_bs_conversion`	None
\|\|	MethylDackel	Uniq. CpG	Total Number Of Unique C's In CpG Context	`unique_cpg`	None
\|\|	MethylDackel	Avg. CpG Coverage	Average CpG Coverage	`average_cpg_coverage`	None

Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

Trimmed Sequence Lengths

This plot shows the number of reads with certain lengths of adapter trimmed.

Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

See the cutadapt documentation for more information on how these numbers are generated.

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Filtered Reads

This plot shows the number of reads (single-end) or read pairs (paired-end) passing filters.

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FastQC (trimmed)

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

This section of the report shows FastQC results after adapter and quality trimming.

Sequence Quality Histograms

The mean quality value across each base position in the read.

To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

Taken from the FastQC help:

The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

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Per Sequence Quality Scores

The number of reads with average quality scores. Shows if a subset of reads has poor quality.

From the FastQC help:

The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

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Per Base Sequence Content

The proportion of each base position for which each of the four normal DNA bases has been called.

To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

To see the data as a line plot, as in the original FastQC graph, click on a sample track.

From the FastQC help:

Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

Click a sample row to see a line plot for that dataset.

Rollover for sample name

Position: -

%T: -

%C: -

%A: -

%G: -

Per Sequence GC Content

The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

From the FastQC help:

This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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Overrepresented sequences

The total amount of overrepresented sequences found in each library.

FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

From the FastQC Help:

A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

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Adapter Content

The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

Note that only samples with ≥ 0.1% adapter contamination are shown.

There may be several lines per sample, as one is shown for each adapter detected in the file.

From the FastQC Help:

The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

No samples found with any adapter contamination > 0.1%

Bismark

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

Alignment Rates

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Strand Alignment

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M-Bias

This plot shows the average percentage methylation and coverage across reads. See the bismark user guide for more information on how these numbers are generated.

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Insert Size

This section of the report has a plot, generated by Picard, that shows the number of reads at a given insert size. Reads with different orientation are summed.

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CpG Coverage

CpG Coverage shows the distribution of the detected CpG coverage in each library.

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Genomic Region Coverage

This section presents the percentage of a certain type of genomic functional region that is covered in each RRBS library, categorized by coverage. The genomic functional region of interest includes CpG islands, gene promoters, and gene bodies. These regions are derived from public annotation files of the reference assemblies.

Gene Body

Gene Body Coverage shows the distribution of the number of individual CpG methylation measurements in gene bodies genome wide.

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Promoter

Promoter Coverage shows the distribution of the number of individual CpG methylation measurements in promoters genome wide.

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CpG Island

CpG Island Coverage shows the distribution of the number of individual CpG methylation measurements in GpG islands genome wide.

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Promoter Profile

Accumulated view of the distribution of methylation percentages around annotated genes. Distances on the x-axis are relative to the nearest TSS. Promoter methylation values were generated using deepTools.

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Bismark (spike-in)

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

This section of the report shows Bismark results for spike-in reads.

Strand Alignment

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Samtools (spike-in)

Samtools is a suite of programs for interacting with high-throughput sequencing data.

This section of the report shows Samtools results for spike-in reads.

Mapped reads per contig

The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

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MethylDackel (spike-in)

MethylDackel is a per-base methylation metrics extraction tool for BAM file with BS-seq alignments.

This section of the report shows the average methylation ratio per contig for spike-in reads.

Correlation Scatter Plot

This plot shows the correlation trend between observed and expected values.

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Correlation Table

This table shows the Pearson's Correlation Coefficient for each sample.

Showing ⁸³/₈₃ rows.

Sample Name	Correlation Coefficient
in3670_13	0.993
in3670_14	0.992
in3670_15	0.976
in3670_16	0.988
in3670_17	0.979
in3670_18	0.976
zr9490_109	0.984
zr9490_119	0.992
zr9490_17	0.990
zr9490_181	0.955
zr9490_182	0.984
zr9490_183	0.969
zr9490_184	0.986
zr9490_185	0.986
zr9490_187	0.977
zr9490_189	0.990
zr9490_19	0.985
zr9490_190	0.992
zr9490_191	0.990
zr9490_192	0.989
zr9490_193	0.985
zr9490_194	0.992
zr9490_195	0.976
zr9490_196	0.989
zr9490_197	0.995
zr9490_198	0.992
zr9490_199	0.990
zr9490_200	0.989
zr9490_201	0.985
zr9490_202	0.992
zr9490_203	0.979
zr9490_204	0.979
zr9490_205	0.993
zr9490_206	0.991
zr9490_25	0.991
zr9490_26	0.987
zr9490_3	0.984
zr9490_32	0.998
zr9490_33	0.992
zr9490_34	0.994
zr9490_35	0.996
zr9490_36	0.997
zr9490_4	0.992
zr9490_41	0.992
zr9490_43	0.987
zr9490_46	0.994
zr9490_47	0.993
zr9490_48	0.992
zr9490_49	0.994
zr9490_50	0.997
zr9490_51	0.997
zr9490_52	0.994
zr9490_53	0.993
zr9490_54	0.991
zr9490_55	0.989
zr9490_56	0.996
zr9490_58	0.997
zr9490_59	0.998
zr9490_60	0.994
zr9490_61	0.993
zr9490_62	0.990
zr9490_63	0.997
zr9490_64	0.989
zr9490_65	0.982
zr9490_68	0.989
zr9490_69	0.981
zr9490_73	0.998
zr9490_74	0.997
zr9490_75	0.993
zr9490_76	0.987
zr9490_77	0.995
zr9490_79	0.984
zr9490_80	0.997
zr9490_81	0.998
zr9490_82	0.998
zr9490_83	0.993
zr9490_84	0.992
zr9490_85	0.996
zr9490_86	0.989
zr9490_87	0.991
zr9490_88	0.991
zr9490_89	0.977
zr9490_90	0.988

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			Correlation Coefficient	Correlation Coefficient	`coefficient`	None

Download

This section contains links to download trimmed fastq files, data and/or images generated by various bioinformatics tools. To download individual files, click on the corresponding links. The links will expire in 90 days.

Showing ⁸³/₈₃ rows and ⁶/₆ columns.

Sample Name	Trimmed Fastq R1	Trimmed Fastq R2	Alignment	DNA Methylation Calling	Browser Track	Methylation Distribution
in3670_13	Download	Download	Download	Download	Download	Download
in3670_14	Download	Download	Download	Download	Download	Download
in3670_15	Download	Download	Download	Download	Download	Download
in3670_16	Download	Download	Download	Download	Download	Download
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zr9490_89	Download	Download	Download	Download	Download	Download
zr9490_90	Download	Download	Download	Download	Download	Download

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Trimmed Fastq R1	Trimmed fastq files.	`tr1`	None
\|\|	Trimmed Fastq R2	Trimmed fastq files.	`tr2`	None
\|\|	Alignment	Aligned sequence reads of individual samples in bam format.	`bam`	None
\|\|	DNA Methylation Calling	Methylation calling results in bedgraph format.	`bedgraph`	None
\|\|	Browser Track	Genome tracks for individual samples that includes methylation ratio and coverage in BigBed format.	`bigbed`	None
\|\|	Methylation Distribution	The overall methylation level in three genomic features of individual sample.	`violinplot`	None

Instructions to download all files

Click here to obtain the code to download all the files. We assume it is in your Download folder.

Find and open Terminal (Mac/Linux) or Windows Powershell (Windows).

Type cd ~/Download and Enter. If the code is downloaded to a different location, change ~/Download to the path to that folder.

Type bash download_links.ps1 (Mac/Linux) or Powershell.exe -ExecutionPolicy Bypass -File .\download_links.ps1 (Windows) and Enter.

Summary

Library Type: Methyl-MiniSeq
Directionality: Non-directional
Genome: hg19
Trimming: 5'R1: 0bp / 5'R2: 0bp / Illumina adapter / RRBS: On

Software Versions

Versions are collected at run time from the software output.

fastqc: 0.11.9
trimgalore: 0.6.4_dev
bismark: 0.22.3
picard: 2.23.8
samtools: 1.9
methyldackel: 0.5.0
ucsc-bedgraphtobigwig: 377
deeptools: 3.5.1
nextflow: 21.10.6
pipeline: null

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Methyl-MiniSeq Analysis Report for in0007_batch4

MultiQC Toolbox

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About MultiQC

Methyl-MiniSeq Analysis Report for in0007_batch4

General Statistics

General Statistics: Columns

Cutadapt

Trimmed Sequence Lengths Help

Filtered Reads

FastQC (trimmed)

Sequence Quality Histograms Help

Per Sequence Quality Scores Help

Per Base Sequence Content Help

Rollover for sample name

Per Sequence GC Content Help

Overrepresented sequences Help

Adapter Content Help

Bismark

Alignment Rates

Strand Alignment

M-Bias

Insert Size

CpG Coverage

Genomic Region Coverage

Gene Body

Promoter

CpG Island

Promoter Profile

Bismark (spike-in)

Strand Alignment

Samtools (spike-in)

Mapped reads per contig

MethylDackel (spike-in)

Correlation Scatter Plot

Correlation Table

Table Ecxg: Columns

Download

Table Dabo: Columns

Instructions to download all files

Summary

Software Versions

Powered by

v1.9

Highlight Samples

Rename Samples

Show / Hide Samples

Trimmed Sequence Lengths

Sequence Quality Histograms

Per Sequence Quality Scores

Per Base Sequence Content

Per Sequence GC Content

Overrepresented sequences

Adapter Content