Table 1.

Read analysis and CpG methylation with intermediate methylation levels.

							Reads unmethylated(< 20% meth.)		Reads methylated(≥ 80% meth.)		Reads partially methylated (≥ 20% and < 80% meth)		CpG methylation
CGI_ID	Genomic coordinates	Ancestral gene	Mean meth. [%]	Mean cov.	Number reads	Mean mapping quality of all reads***	[#]	[%]	[#]	[%]	[#]	[%]	VAR	SD
2391_1_hg19	chr1:240656253-240656720	GREM1	56%	12	83	60	29	35%	44	53%	10	12%	0.04	0.2
6141_1_hg19	chr4:144833114-144833512	SAV1	49%	18	111	57	67	60%	39	35%	5	5%	0.04	0.2
9224_1_hg19**	chr7:16890768-16891087	ARHGAP20	58%	13	62	59	24	39%	27	44%	11	18%	0.06	0.23
9261_1_hg19	chr7:23530434-23530690	RPS2	72%	15	59	60	16	27%	40	68%	3	5%	0.01	0.11
9377_1_hg19	chr7:36010997-36011407	PPP1R14B	39%	7	48	60	25	52%	15	31%	8	17%	0.04	0.21
9473_1_hg19	chr7:52341468-52342266	CCDC115	79%	12	108	56	19	18%	74	69%	15	14%	0.03	0.17
13085_1_hg19	chr10:66813635-66814061	NEK4	76%	8	58	49	9	16%	40	69%	9	16%	0.02	0.16
13250_1_hg19	chr10:91596974-91597792	MARK2	22%	10	109	58	83	76%	23	21%	3	3%	0.01	0.07
14414_1_hg19*	chr11:62138621-62138873	ASRGL	55%	10	40	58	17	43%	21	53%	2	5%	0.02	0.13
15224_1_hg19*	chr12:3947922-3948620	PARP11	42%	11	108	49	53	49%	45	42%	10	9%	0.05	0.20
15400_1_hg19	chr12:31405184-31405545	RPL13AP5	69%	16	97	53	26	27%	61	63%	10	10%	0.02	0.15
15512_1_hg19	chr12:49782965-49783193	FGFR1OP2	54%	18	59	60	22	37%	30	51%	7	12%	0.02	0.15
16448_1_hg19	chr13:21893156-21893605	GRK6	79%	13	88	58	9	10%	67	76%	12	14%	0.02	0.12
16458_1_hg19	chr13:23412207-23412623	IPMK	31%	11	66	59	41	62%	17	26%	8	12%	0.02	0.15
16634_1_hg19*	chr13:48892635-48893857	PPP1R26	75%	13	193	60	69	36%	116	60%	8	4%	0.02	0.13
17031_1_hg19	chr14:21191657-21191860	XPO6	42%	7	30	60	18	60%	11	37%	1	3%	0.02	0.16
19100_1_hg19*	chr16:15083366-15084045	KIAA2013	75%	11	104	44	22	21%	67	64%	15	14%	0.02	0.16
20403_1_hg19	chr17:15686218-15686474	IL6ST	20%	13	49	57	41	84%	7	14%	2	4%	0.01	0.10
23548_1_hg19	chr19:21860792-21861016	MTDH	59%	14	52	59	14	27%	27	52%	11	21%**	0.03	0.17
24982_1_hg19	chr20:30135076-30135292	MCTS1	55%	20	64	60	25	39%	37	58%	2	3%	0.01	0.10
26859_1_hg19	chrX:37026348-37026706	FAM47A	77%	8	44	46	6	14%	34	77%	4	9%	0.02	0.15

This table shows the results of the read methylation and CpG methylation analysis of 17 CGIs overlapping a retrogene and containing an intermediate methylation level and four already published CGIs by Rademacher et al. (same dataset; indicated by *).²⁰ In addition to CGI_ID, genome coordinates, ancestral gene, mean methylation, mean coverage the number of reads is shown. The reads are divided into three classes, unmethylated (< 20% methylation), methylated (≥ 80% methylation) and partially methylated (≥ 20% and < 80% methylation). For each class, the total number of reads and the percentage is shown. The last column shows the results of the CpG methylation analyses; variance (VAR) and standard derivation (SD) over all single CpGs were calculated. More information of the CGIs, retrocopies, and ancestral genes can be found in the supplemental material (Table S11).

^*Published by Rademacher et al.²⁰

^**Fulfill only one criteria (out of two) described by Rademacher et al.²⁰

^***Mean of the phred quality score of all analyzed reads. The score quantifies the probability that a read is misplaced (for further information see supplement material).