Table 1 Diurnal APAs from genes with ≥2 APA sites (20 lowest median meta2d p-values)

PAS_ID	Symbol	Chromosome	Strand	Peak	PASs/gene	Total	median p	median BH.Q	AVE phase	AVE Amp	AVE rAmp
497,844	Parvb	7	+	115,445,766	2	6707	1.30E-10	1.91E-06	1.89	373	0.29
251,968	Dnajb1	19	-	24,522,731	2	4379	1.09E-09	6.93E-06	15.54	194	0.24
424,776	Ccdc107	5	+	57,752,233	3	1833	1.13E-08	4.15E-05	18.14	124	0.37
282,515	Rap1gds1	2	-	227,512,038	2	45	8.29E-09	3.62E-05	18.35	10	1.29
86,566	Hint1	10	+	38,993,254	3	44,628	1.01E-08	3.73E-05	11.56	1871	0.22
42,414	Dbp	1	+	96,180,614	2	5424	2.19E-08	5.35E-05	11.88	408	0.40
496,957	Cacna1i	7	+	111,947,418	3	2361	3.52E-08	7.46E-05	0.81	112	0.24
301,149	S100a10	2	+	179,229,660	2	863	4.75E-08	9.48E-05	21.50	88	0.59
249,570	Ndrg4	19	-	9,351,408	2	57,912	5.93E-08	1.11E-04	0.75	2119	0.19
141,758	Iars2	13	-	96,831,484	3	263	5.83E-08	9.74E-05	18.22	33	0.73
89,040	Phf23	10	+	54,722,784	2	2014	7.00E-08	1.15E-04	13.48	119	0.32
455,360	Wdr35	6	+	31,831,183	5	154	6.21E-08	9.86E-05	18.05	23	0.83
279,711	Prpf38b	2	-	196,553,983	3	397	1.05E-07	1.47E-04	19.09	34	0.48
363,773	Cacna2d1	4	-	18,950,614	2	3218	1.05E-07	1.51E-04	5.00	248	0.39
309,907	Cbs	20	-	9,708,260	4	3085	1.65E-07	2.18E-04	21.42	165	0.30
214,595	Faf2	17	-	9,947,225	4	2246	2.24E-07	2.29E-04	15.60	105	0.26
447,907	Syndig1l	6	-	104,323,418	2	253	2.17E-07	2.46E-04	8.92	36	0.77
470,887	Btbd11	7	-	18,035,151	3	3401	3.07E-07	3.36E-04	23.59	184	0.29
449,908	Dicer1	6	-	123,627,529	3	296	3.65E-07	4.14E-04	17.00	30	0.58
549,543	Coq10b	9	+	56,573,671	2	334	2.07E-07	2.43E-04	16.60	32	0.54

PAS_ID is a unique identifier for each PAS. Gene Symbol, Chromosome are listed, as well as Strand according to the convention of each chromosome. Peak is the mode or most common 3′ endpoint in the cluster. The number of PASs per gene is listed. Total refers to the sum of the reads for all samples.
Meta2d calculations shown are: median p median probability of cycling, median BH.Q median Benjamini/Hochberg adjusted probability, AVE phase average peak phase, AVE Amp average amplitude (from peak to trough) of reads, and AVE rAmp average relative amplitude adjusted by the mean read number.

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