Table 1.

Relationship between sequence identity and aCGH signal

Chr	385K-aCGH					2.1M-aCGH					3.1M-aCGH
	Probe count		Test signal			Probe count		Test signal			Probe count		Test signal
	M	MM	M	MM	P-value	M	MM	M	MM	P-value	M	MM	M	MM	P-value
1	13 188	16 205	4655	4489	8.90E-15	72 049	91 734	3550	3331	1.56E-82	101 963	124 620	3266	3120	2.60E-44
2	13 909	13 990	4612	4455	1.30E-12	76 513	77 565	3516	3463	5.04E-06	111 127	114 313	2999	2854	2.80E-48
3	11 306	11 954	4682	4485	7.70E-16	64 400	67 515	3427	3316	9.24E-20	85 703	90 427	2494	2422	2.00E-12
4	8747	13 700	4628	4434	4.00E-15	48 344	78 238	3612	3351	3.07E-81	72 101	111 243	2508	2427	4.50E-16
5	9935	12 574	4646	4505	1.20E-07	55 891	69 525	3601	3497	2.35E-14	79 773	102 559	2703	2629	1.70E-15
6	12 095	10 437	4661	4414	1.60E-27	67 247	57 338	3205	3113	1.49E-14	94 546	82 567	2865	2772	3.20E-19
7	8542	11 126	4626	4359	8.40E-21	48 250	63 624	3334	3029	6.48E-116	74 732	93 915	3606	3450	1.60E-21
8	7962	11 620	4662	4379	2.40E-23	43 465	65 059	3303	2986	3.81E-124	65 419	94 888	3646	3422	1.20E-39
9	7903	11 389	4617	4422	2.20E-14	43 317	62 739	3295	3137	9.58E-32	65 014	94 193	2385	2095	7.00E-149
10	13 865	5 569	4670	4562	2.10E-04	77 515	32 036	3139	3183	1.49E-03	106 880	43 868	2011	2000	2.60E-01
11	11 058	8255	4567	4438	5.40E-06	62 019	44 518	3311	3210	3.13E-13	95 181	69 851	2445	2453	5.00E-01
12	8686	7689	4660	4417	1.60E-17	50 261	43 365	3057	2972	6.60E-10	69 487	61 473	3193	3220	1.60E-01
13	9250	8121	4671	4507	2.60E-08	51 745	45 216	3062	2916	7.69E-28	75 538	63 704	3269	3193	8.30E-06
14	7982	9259	4682	4389	4.90E-23	46 043	51 318	2918	2820	2.87E-13	60 075	73 647	2674	2683	5.10E-01
15	7888	7931	4637	4388	4.60E-16	43 200	43 898	3073	2814	1.34E-71	63 517	62 254	2512	2365	1.90E-42
16	7768	6861	4616	4563	7.70E-02	44 036	37 931	2967	2856	4.09E-15	60 921	51 324	2474	2465	4.20E-01
17	5464	8188	4642	4486	1.10E-05	30 042	46 894	3025	2958	1.72E-05	42 824	67 144	2851	2708	1.80E-23
18	6324	7615	4707	4538	4.80E-08	34 739	41 374	2999	2980	1.93E-01	48 748	60 966	3124	3053	9.70E-07
19	7336	1773	4645	4490	1.10E-03	40 292	9748	3111	3008	2.57E-05	60 703	14 985	3078	3055	3.20E-01

MM, regions of high polymorphism between C57BL/6J and 129X1/SvJ (‘mismatched’); M, non-polymorphic regions (‘matched’). Probe count columns contain the number of probes within M and MM regions. Test signal columns contain the mean, single channel, linear-scale aCGH intensities of the M and MM regions. The P-value is the result of a t-test, testing the difference of the mean signals of M and MM probes, as described in the Methods section.