Order	SeqName	SeqType	IsAE	Lum_Epi	Lum_Epi2	Myo_Epi	Myo_Epi2	hESCs	StemLike	vHMECs
1	NPHP3	Gene	0	46.10	17.75	58.33	35.06	42.84	32.72	50.23
2	393156	Transcript	0	0	0	0	0	0	0	0
3	326682	Transcript	1	34.23	28.95	33.71	20.54	3.99	18.33	3.00
4	393144	Transcript	1	19.98	25.19	32.19	33.02	12.52	21.12	4.14
5	343113	Transcript	1	10.28	8.68	15.33	14.56	0.42	7.50	3.51
6	337331	Transcript	0	48.58	19.04	57.83	30.71	46.33	44.54	44.18
7	383282	Transcript	0	1.84	3.55	0.00	2.86	0.00	5.43	3.11
8	355458	Transcript	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
9	264990	Transcript	0	25.45	10.00	23.37	14.53	34.76	20.15	41.72
10	IG37_AR15	ActiveIntergenicRegion	0	0.59	0.00	0.99	0.91	10.14	0.00	0.00
11	ER1a	ExonRegion	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
12	ER1b	ExonRegion	0	1.14	0.77	0.00	0.00	0.00	0.78	0.00
13	E1_Ac	KnownBoundary	0	3.22	2.31	0.85	0.00	0.00	2.17	0.00
14	ER1c	ExonRegion	0	4.22	11.81	9.46	18.84	1.43	14.84	7.54
15	E1a_E2a	KnownJunction	0	2.64	4.26	0.00	4.20	0.00	8.01	4.76
16	E1a_E3a	KnownJunction	1	10.53	18.63	33.60	22.35	8.94	32.59	24.87
17	ER2a	ExonRegion	0	1.05	2.83	0.00	1.52	0.00	2.84	1.46
18	E2_Da	NovelBoundary	0	2.92	10.80	6.94	8.48	2.12	2.81	2.06
19	ER3a	ExonRegion	0	25.54	33.29	64.81	47.74	20.06	39.58	33.41
20	E3a_E4a	KnownJunction	1	27.32	21.41	80.98	51.36	17.96	46.69	38.74
21	ER4a	ExonRegion	0	36.42	24.59	79.83	54.51	25.57	36.28	41.22
22	E4_Da	NovelBoundary	0	6.36	4.44	10.19	9.59	3.14	8.44	2.72
23	E4a_E5a	KnownJunction	1	14.92	11.17	20.94	21.78	0.00	11.15	5.25
24	E4a_E6a	KnownJunction	1	11.92	12.22	49.42	24.49	24.37	15.46	28.72
25	I4_SR1	SilentIntronRegion	0	8.35	3.28	14.57	3.93	2.93	3.28	4.25
26	ER5a	ExonRegion	0	5.64	6.20	9.71	7.33	0.84	3.85	1.78
27	E5_Da	NovelBoundary	1	19.58	4.20	23.85	19.13	3.32	8.82	2.82
28	I5	Intron	0	13.41	3.63	16.53	6.94	2.40	6.06	2.91
29	I5_SR1	SilentIntronRegion	0	15.35	3.62	15.83	7.10	2.75	7.35	2.62
30	I5_AR2	ActiveIntronRegion	0	9.37	3.75	18.56	6.77	1.66	3.33	3.64
31	E6_Aa	NovelBoundary	1	11.17	6.99	16.11	15.47	2.12	3.94	8.58
32	ER6a	ExonRegion	1	27.03	23.97	73.73	47.71	32.26	29.86	44.09
33	E6a_E7a	KnownJunction	0	35.32	28.16	67.86	45.46	28.72	27.93	45.80
34	ER7a	ExonRegion	0	44.97	39.29	91.56	63.33	37.22	40.42	63.11
35	E7a_E8a	KnownJunction	1	51.61	49.34	110.26	56.19	34.10	40.47	46.72
36	ER8a	ExonRegion	0	55.22	33.22	107.40	45.56	38.04	44.42	56.21
37	E8a_E10a	KnownJunction	0	46.33	20.73	93.72	34.78	30.11	48.11	52.41
38	ER9a	ExonRegion	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
39	ER10a	ExonRegion	0	41.62	21.91	94.78	44.15	33.39	42.15	56.03
40	E10a_E11a	KnownJunction	0	40.56	18.52	85.20	59.79	31.67	34.65	68.13
41	ER11a	ExonRegion	1	38.16	17.57	110.21	49.71	47.37	34.34	74.03
42	E11a_E12a	KnownJunction	1	39.14	16.29	107.38	32.83	45.78	32.05	70.28
43	ER12a	ExonRegion	0	47.22	25.16	110.59	58.52	42.29	41.44	82.46
44	E12a_E13a	KnownJunction	0	55.84	32.42	113.47	65.40	51.13	43.76	87.08
45	ER13a	ExonRegion	0	43.22	23.74	81.87	46.19	35.77	36.38	60.02
46	E13a_E14a	KnownJunction	0	64.22	32.87	96.78	56.54	49.70	59.15	82.46
47	ER14a	ExonRegion	0	58.40	32.76	98.10	54.89	35.74	50.04	70.95
48	E14a_E15a	KnownJunction	0	42.41	25.82	81.49	58.41	30.52	31.09	53.37
49	ER15a	ExonRegion	0	53.91	25.29	95.13	48.46	44.43	41.16	62.13
50	E15a_E16a	KnownJunction	0	28.04	7.30	65.86	12.08	30.55	21.04	60.88
51	E15a_E17a	KnownJunction	1	19.98	25.19	32.19	33.02	12.52	21.12	4.14
52	ER16a	ExonRegion	0	31.07	11.57	72.07	17.78	38.36	15.01	73.43
53	E16a_E17a	KnownJunction	0	35.70	10.01	79.35	18.34	40.23	15.84	77.68
54	ER17a	ExonRegion	0	65.71	30.22	116.48	51.27	46.55	43.33	73.81
55	E17_Da	NovelBoundary	1	5.09	0.00	15.74	1.68	10.07	1.66	3.88
56	E17a_E18a	KnownJunction	1	22.38	5.73	70.00	25.63	28.47	20.23	61.37
57	E17a_E19a	KnownJunction	1	34.23	28.95	33.71	20.54	3.99	18.33	3.00
58	E18_Aa	NovelBoundary	1	16.02	4.12	42.74	4.28	4.13	0.00	6.33
59	ER18a	ExonRegion	1	29.90	5.44	68.73	27.03	40.82	24.19	73.68
60	E18a_E19a	KnownJunction	1	28.22	2.65	55.64	25.09	41.38	16.32	59.38
61	ER19a	ExonRegion	0	61.73	28.18	106.35	63.47	58.16	46.68	85.42
62	E19a_E20a	KnownJunction	0	65.04	34.68	78.66	75.69	53.74	47.52	103.07
63	ER20a	ExonRegion	0	45.68	26.59	81.45	77.18	41.15	44.40	91.03
64	E20a_E21a	KnownJunction	0	46.46	25.98	71.65	69.73	52.01	51.21	102.74
65	ER21a	ExonRegion	0	51.29	23.73	78.97	71.22	52.27	48.14	81.48
66	E21a_E22a	KnownJunction	0	37.94	20.52	71.64	68.73	59.61	45.75	66.38
67	ER22a	ExonRegion	0	58.68	22.54	79.74	62.59	48.02	46.27	74.18
68	E22a_E23a	KnownJunction	0	76.52	25.27	83.55	74.26	64.71	58.96	59.33
69	ER23a	ExonRegion	0	80.03	29.76	107.64	72.49	63.83	67.48	81.43
70	E23a_E24a	KnownJunction	0	70.11	27.27	88.42	59.00	53.46	79.57	60.19
71	ER24a	ExonRegion	0	76.89	26.41	104.84	52.83	63.25	60.61	65.54
72	E24a_E25a	KnownJunction	1	98.70	44.08	136.14	35.73	66.62	70.05	56.09
73	ER25a	ExonRegion	1	123.76	38.70	148.74	54.49	58.30	62.43	57.03
74	E25a_E26a	KnownJunction	1	118.00	35.10	132.75	51.01	74.23	55.53	56.68
75	ER26a	ExonRegion	0	71.79	29.78	97.09	57.16	56.85	38.76	48.59
76	E26a_E27a	KnownJunction	0	43.29	16.31	70.40	45.35	21.97	24.60	35.08
77	ER27a	ExonRegion	0	54.15	28.80	82.49	53.35	47.10	34.53	57.76
78	E27_Da	NovelBoundary	0	10.66	8.77	10.71	3.06	1.01	7.10	4.41
79	E27a_E28a	KnownJunction	0	45.71	25.30	82.27	52.99	38.94	29.32	50.80
80	E28_Aa	NovelBoundary	0	15.00	5.65	19.28	2.93	5.67	4.21	8.30
81	ER28a	ExonRegion	0	71.03	23.28	94.96	53.26	52.63	41.40	59.21
82	E28a_E29a	KnownJunction	0	67.81	26.67	86.44	62.66	39.79	35.24	65.75
83	ER29a	ExonRegion	0	93.78	19.61	100.19	71.74	59.86	52.51	65.52
84	E29a_E30a	KnownJunction	1	103.54	18.10	105.87	74.58	80.64	68.93	71.83
85	ER30a	ExonRegion	0	78.67	19.93	97.67	53.07	58.88	68.03	68.77
86	E30_Da	KnownBoundary	0	56.90	21.10	76.74	30.45	37.12	38.83	69.52
87	E30a_E32b	KnownJunction	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00
88	ER30b	ExonRegion	0	48.58	19.04	57.83	30.71	46.33	44.54	44.18
89	I30	Intron	1	10.10	5.70	18.03	9.27	16.44	9.12	13.16
90	I30_SR2	SilentIntronRegion	1	11.11	8.56	23.29	14.25	24.33	12.60	19.36
91	I30_SR4	SilentIntronRegion	1	13.79	3.75	19.82	6.97	14.41	10.67	13.79
92	I30_AR3	ActiveIntronRegion	0	16.10	6.28	28.57	9.36	21.64	8.56	15.06
93	Ix	Intron	0	13.51	6.96	26.84	8.37	9.42	7.81	11.03
94	Ix_SR1	SilentIntronRegion	0	18.09	8.74	37.95	9.76	9.58	8.52	13.62
95	Ix_AR1	ActiveIntronRegion	0	13.02	5.71	27.92	7.67	10.94	10.10	9.17
96	I30	Intron	0	13.59	7.06	12.56	17.19	12.33	19.08	6.31
97	I30_AR1	ActiveIntronRegion	0	13.74	7.14	12.68	17.38	12.48	19.30	6.38
98	E31_Aa	NovelBoundary	0	15.91	16.42	16.02	22.84	3.67	36.39	11.64
99	ER31a	ExonRegion	0	26.72	12.78	22.02	21.23	15.44	22.10	22.04
100	E31a_E32a	KnownJunction	1	17.21	13.37	18.51	18.07	18.00	38.11	55.51
101	ER32a	ExonRegion	1	19.47	15.59	27.66	17.87	19.71	37.39	58.24
102	ER32b	ExonRegion	0	26.91	14.10	44.03	23.39	34.50	33.96	55.88
103	E32a_E33a	KnownJunction	1	31.59	12.06	52.67	19.59	44.05	47.65	53.37
104	ER33a	ExonRegion	0	44.12	16.71	53.08	34.98	44.05	42.68	67.54
105	E33a_E34a	KnownJunction	0	50.29	18.65	56.65	26.55	49.66	31.19	91.32
106	ER34a	ExonRegion	0	52.24	19.43	49.20	42.95	55.25	30.20	86.66
107	E34a_E35a	KnownJunction	0	56.83	11.22	48.66	43.40	66.02	23.72	74.44
108	ER35a	ExonRegion	0	69.22	17.24	58.28	45.06	75.95	29.80	78.03
109	E35a_E36a	KnownJunction	1	97.82	20.96	69.88	27.96	80.22	15.57	52.84
110	ER36a	ExonRegion	0	83.10	23.74	71.45	34.51	69.96	30.01	59.20
111	E36a_E37a	KnownJunction	1	99.04	18.89	81.77	30.42	73.12	25.59	51.78
112	ER37a	ExonRegion	0	75.99	14.71	59.01	25.20	68.21	24.25	54.11
113	E37a_E38a	KnownJunction	0	79.94	5.46	56.25	23.16	55.30	21.36	46.08
114	ER38a	ExonRegion	0	73.63	18.30	57.70	28.56	46.62	19.56	50.69
115	E38a_E39a	KnownJunction	0	66.59	17.65	49.19	24.41	38.08	27.68	58.36
116	ER39a	ExonRegion	0	87.87	13.37	56.07	31.91	83.64	27.10	60.97
117	E39a_E40a	KnownJunction	0	1.72	0.00	0.79	4.47	1.18	0.00	0.89
118	E39a_E41a	KnownJunction	0	86.47	12.40	65.34	28.23	100.16	19.86	75.78
119	ER40a	ExonRegion	0	0.57	0.00	0.85	2.83	1.13	0.73	0.78
120	E40a_E41a	KnownJunction	0	0.00	0.00	0.00	1.11	0.00	1.37	0.00
121	ER41a	ExonRegion	0	86.56	14.67	64.91	31.73	82.22	31.25	72.18
122	E41a_E42a	KnownJunction	1	98.82	22.65	47.28	32.97	82.11	29.67	58.31
123	E41a_E43a	NovelJunction	0	0.00	0.00	0.00	1.60	17.24	0.00	0.00
124	ER42a	ExonRegion	0	108.50	17.08	69.33	36.55	110.38	26.09	80.04
125	E42a_E43a	KnownJunction	0	105.33	11.09	70.50	37.06	85.78	26.37	69.65
126	ER43a	ExonRegion	0	82.29	15.93	54.02	34.30	83.37	25.54	75.75
127	E43a_E44a	KnownJunction	0	71.17	25.27	57.22	38.58	98.60	31.65	77.42
128	ER44a	ExonRegion	0	90.16	20.05	73.44	36.84	100.79	23.19	92.68
129	E44a_E45a	KnownJunction	0	76.61	15.24	57.70	12.98	80.71	24.25	77.53
130	I44_AR2	ActiveIntronRegion	0	2.77	3.44	2.42	3.42	10.26	0.76	4.16
131	ER45a	ExonRegion	0	45.36	10.08	41.06	8.80	88.25	17.57	67.38
132	E45_Da	KnownBoundary	1	9.90	0.00	17.34	1.25	9.71	1.58	1.38
133	E45a_E45b	KnownJunction	1	1.70	5.83	5.19	1.44	54.01	2.84	37.72
134	ER45b	ExonRegion	1	16.20	2.28	16.11	4.34	7.55	4.58	8.19
135	E45_Ab	KnownBoundary	1	22.26	7.72	40.29	18.12	5.88	11.90	13.39
136	ER45c	ExonRegion	0	39.02	10.99	44.18	21.80	62.28	20.27	54.57
137	E45b_E46a	KnownJunction	0	36.68	8.56	40.52	32.59	55.65	28.97	53.10
138	ER46a	ExonRegion	0	30.89	8.23	32.00	24.19	45.84	24.18	47.21
139	E46a_E47a	KnownJunction	0	29.37	14.42	39.92	19.59	34.81	20.61	49.17
140	ER47a	ExonRegion	0	38.00	10.79	36.93	28.69	46.62	28.78	57.18
141	E47a_E48a	KnownJunction	0	32.61	10.19	26.54	15.74	57.10	18.60	50.03
142	ER48a	ExonRegion	0	34.11	12.26	34.34	26.83	60.46	25.54	69.62
143	E48a_E49a	KnownJunction	1	32.23	6.62	34.59	30.42	66.07	20.31	71.36
144	ER49a	ExonRegion	0	28.50	10.06	27.46	24.55	57.20	15.72	62.19
145	E49a_E50a	KnownJunction	0	36.08	8.28	31.43	17.04	65.33	13.40	65.82
146	ER50a	ExonRegion	0	32.71	11.20	28.34	21.19	45.39	27.75	45.28
147	ER50b	ExonRegion	0	1.15	0.00	1.52	0.31	1.21	0.61	1.01