Table 3.

Read Analysis and CpG Methylation of CGIs with Intermediate Methylation Levels (Methylome 1)

CGI_ID	Gene	Chr.	Length (bp)	Mean Methylation (%)	Mean Coverage	Number of Reads	Reads Unmethylated (<20% methylation)		Reads Methylated (>80% methylation)		Reads Partially Methylated (≥20% and <80% methylation)		CpG Methylation
							(Number)	(%)	(Number)	(%)	(Number)	(%)	VAR	SD
1911_1_hg19	DCAF	1	214	81	18	70	2	3	48	69	20	29	0.01	0.11
4675_1_hg19	GXYLT2	3	326	73	19	108	8	7	70	65	30	28	0.02	0.12
4754_1_hg19	SLC9C1	3	463	32	9	66	31	47	15	23	20	30	0.09	0.29
9009_1_hg19	MAD1L1	7	210	78	8	24	2	8	14	58	8	33	0.08	0.29
14414_1_hg19	ASRGL1	11	252	55	10	40	17	43	21	53	2	5	0.02	0.13
15205_1_hg19	CACNA2D4	12	1219	84	12	188	7	4	143	76	38	20	0.03	0.18
15224_1_hg19	PARP11	12	698	42	11	108	53	49	45	42	10	9	0.05	0.21
15290_1_hg19	CD163L1	12	624	23	14	153	57	37	41	27	55	36	0.08	0.27
16634_1_hg19	RB1	13	1222	63	13	193	69	36	116	60	8	4	0.02	0.13
19100_1_hg19	PDXDC1	16	679	75	11	104	22	21	67	64	15	14	0.02	0.16
19870_1_hg19	SLC7A5	16	207	58	15	45	17	38	17	38	11	24	0.19	0.44
20632_1_hg19	MYO1D	17	466	22	7	54	38	70	11	20	5	9	0.03	0.18
20636_1_hg19	ASIC2	17	506	58	6	44	4	9	20	45	20	45	0.08	0.29
25767_1_hg19	HSF2BP	21	403	70	17	93	22	24	50	54	21	23	0.10	0.32

Note.—This table shows the results of the read methylation and CpG methylation analysis of 14 candidate CGIs of methylome 1 (for methylome 2, see supplementary table S2, Supplementary Material online). In addition to CGI_ID, gene, chromosome, length, mean methylation, mean coverage, and number of reads, the reads are divided into three classes: Unmethylated, methylated, and partially methylated. The last column shows the results of the CpG methylation analyses, variance (VAR), and standard derivation (SD) over all single CpGs were calculated. Bold: CGIs that might be differentially methylated (partially methylated reads ≤20% and VAR ≤0.05).