. 2016 Aug 29;113(37):10400–10405. doi: 10.1073/pnas.1601060113

Table S3.

Number of reads from Reyes, Minot, and Norman datasets recruited to ALL contigs dataset

Cohort	Individual	Total reads	Total reads used	% Reads used	Total unique reads^*	% Unique reads^*	Unique reads used	% Unique reads used
Minot	Healthy^†	907,909	112,535	11	904,562	100	NA	NA
Reyes	Healthy^†	1,318,248	348,747	28	1,229,707	93	NA	NA
Boston	Healthy 1	1,855,868	151,886	8.18	751,022	40	30,162	4
Boston	Healthy 2	3,077,606	919,913	29.89	1,459,460	47	322,958	22
Boston	Healthy 3	2,363,534	431,989	18.28	1,415,938	60	235,284	17
Boston	Healthy 4	2,545,426	174,344	6.85	1,138,171	45	75,142	7
Boston	Healthy 5	3,594,714	1,987,264	55.28	1,829,231	51	617,223	34
Boston	Healthy 6	3,032,490	869,133	28.66	1,184,156	39	144,158	12
Boston	Healthy 7	2,754,790	830,673	30.15	1,943,469	71	395,908	20
Boston	Healthy 8	2,736,014	6,236	0.23	1,208,815	44	2,166	0
Boston	Healthy 9	2,677,362	1,165,711	43.54	2,031,749	76	575,048	28
Boston	Healthy 10	1,217,356	37,264	3.06	704,349	58	28,478	4
Boston	Healthy 11	3,963,300	165,613	4.18	2,243,045	57	68,805	3
Boston	Healthy 12	3,410,232	3,095	0.09	1,516,125	44	1,582	0
Boston	Healthy 13	3,212,322	1,384,980	43.11	1,764,791	55	326,411	18
Boston	Healthy 14	2,035,696	1,366,499	67.12	1,197,715	59	530,039	44
Boston	Healthy 15	1,435,100	357,568	24.91	891,091	62	192,196	22
Boston	Healthy 16	5,688,510	837,832	14.73	3,207,930	56	240,724	8
Boston	Healthy 17	4,192,464	647,346	15.44	2,366,494	56	67,784	3
Boston	Healthy 18	2,612,060	56,094	2.15	1,430,980	55	17,392	1
Boston	Healthy 19	2,774,234	276,275	9.96	1,282,998	46	206,015	16
Boston	Healthy 20	3,741,796	860,840	23.00	1,823,341	49	184,955	10
Cambridge	Healthy 21	813,036	40,290	4.95	362,723	45	30,453	8
Cambridge	Healthy 22	2,191,674	53,945	2.46	798,150	36	12,521	2
Cambridge	Healthy 23	3,987,976	1,259,661	31.59	1,487,481	37	212,936	14
Cambridge	Healthy 24	744,306	96,954	13.02	520,367	70	53,508	10
Cambridge	Healthy 25	1,412,874	9,063	0.64	429,886	30	6,229	1
Cambridge	Healthy 26	2,148,478	20,278	0.94	1,200,855	56	14,646	1
Cambridge	Healthy 27	2,167,272	695,799	32.10	1,261,182	58	364,978	29
Cambridge	Healthy 28	1,982,540	145,999	7.36	734,000	37	15,439	2
Cambridge	Healthy 29	2,456,352	1,699,167	69.17	1,325,059	54	562,147	42
Cambridge	Healthy 30	2,205,292	343,671	15.58	1,183,795	54	144,100	12
Cambridge	Healthy 31	2,242,066	6,184	0.27	979,536	44	4,666	0
Cambridge	Healthy 32	1,666,460	618,605	37.12	1,013,793	61	266,076	26
Cambridge	Healthy 33	873,858	2,584	0.29	391,024	45	1,836	0
Cambridge	Healthy 34	889,734	34,762	3.90	399,021	45	14,981	4
Cambridge	Healthy 35	2,477,270	82,617	3.33	864,305	35	49,443	6
Cambridge	Healthy 36	2,755,938	1,066,225	38.69	1,458,486	53	251,497	17
Cambridge	Healthy 37	2,747,478	160,672	5.85	1,227,408	45	64,346	5
Cambridge	Healthy 38	2,964,822	600,366	20.25	1,263,739	43	143,055	11
Cambridge	Healthy 39	3,169,706	511,639	16.14	1,242,348	39	128,583	10
Cambridge	Healthy 40	3,101,720	225,445	7.27	953,805	31	47,335	5
Cambridge	Healthy 41	3,488,468	170,214	4.88	2,002,130	57	129,009	6
Chicago	Healthy 42	2,403,326	14,722	0.61	1,391,663	58	5,223	0
Chicago	Healthy 43	2,410,296	509,131	21.12	1,345,791	56	95,852	7
Chicago	Healthy 44	2,368,680	580,817	24.52	1,321,717	56	133,899	10
Chicago	Healthy 45	2,213,436	530,977	23.99	1,395,454	63	289,514	21
Chicago	Healthy 46	3,332,532	72,812	2.18	1,983,779	60	22,311	1
Chicago	Healthy 47	1,886,752	1,195,555	63.36	601,889	32	92,555	15
Chicago	Healthy 48	2,414,120	307,535	12.74	1,347,958	56	193,963	14
Chicago	Healthy 49	1,892,214	4,268	0.22	511,371	27	3,383	1
Chicago	Healthy 50	2,731,028	180,879	6.62	1,702,024	62	58,545	3
Chicago	Healthy 51	1,968,640	185,476	9.42	1,191,892	61	37,410	3
Chicago	Healthy 52	1,981,600	19,512	0.98	1,374,198	69	8,691	1
Chicago	Healthy 53	2,704,256	101,438	3.75	2,047,476	76	53,442	3
Chicago	Healthy 54	2,699,190	205,790	7.62	1,470,581	54	38,420	3
Chicago	Healthy 55	2,733,304	72,812	2.66	1,624,789	59	56,216	3
Chicago	Healthy 56	2,574,044	581,983	22.61	1,301,623	51	123,267	9
Chicago	Healthy 57	2,658,816	664,954	25.01	1,496,994	56	295,962	20
Chicago	Healthy 58	2,182,842	112,919	5.17	1,481,366	68	90,999	6
Chicago	Healthy 59	2,426,646	444,779	18.33	1,598,184	66	332,880	21
Chicago	Healthy 60	1,590,130	468,032	29.43	742,336	47	79,208	11
Chicago	Healthy 61	1,570,368	477,413	30.40	1,108,109	71	268,227	24
Chicago	Healthy 62	1,441,054	2,383	0.16	700,849	49	1,598	0
Boston	Disease 1	2,388,256	24,222	1.01	NA	NA	22,654	NA
Boston	Disease 2	2,363,664	1,398,078	59.15	NA	NA	574,102	NA
Boston	Disease 3	2,575,262	1,589,148	61.71	NA	NA	730,253	NA
Boston	Disease 4	2,134,480	94,343	4.42	NA	NA	62,443	NA
Boston	Disease 5	2,453,782	54,306	2.21	NA	NA	43,918	NA
Boston	Disease 6	1,416,910	58,142	4.10	NA	NA	51,045	NA
Boston	Disease 7	2,183,796	100,330	4.59	NA	NA	44,764	NA
Boston	Disease 8	2,992,536	803,376	26.85	NA	NA	315,793	NA
Boston	Disease 9	3,079,596	109,046	3.54	NA	NA	86,546	NA
Boston	Disease 10	1,209,042	153,107	12.66	NA	NA	49,222	NA
Boston	Disease 11	2,651,402	929,362	35.05	NA	NA	541,354	NA
Boston	Disease 12	2,112,430	14,213	0.67	NA	NA	10,424	NA
Boston	Disease 13	2,506,052	3,550	0.14	NA	NA	2,768	NA
Boston	Disease 14	835,412	143,716	17.20	NA	NA	91,479	NA
Boston	Disease 15	614,422	104,165	16.95	NA	NA	47,673	NA
Boston	Disease 16	2,773,122	107,708	3.88	NA	NA	55,308	NA
Boston	Disease 17	2,349,140	416,753	17.74	NA	NA	289,689	NA
Boston	Disease 18	4,892,418	118,074	2.41	NA	NA	47,234	NA
Boston	Disease 19	3,930,552	6,221	0.16	NA	NA	5,446	NA
Boston	Disease 20	3,374,786	194,894	5.78	NA	NA	106,648	NA
Boston	Disease 21	1,162,722	4,247	0.37	NA	NA	4,154	NA
Boston	Disease 22	2,123,106	1,384,249	65.20	NA	NA	595,006	NA
Boston	Disease 23	2,969,610	1,806,143	60.82	NA	NA	971,425	NA
Boston	Disease 24	1,213,940	1,195	0.10	NA	NA	1,099	NA
Boston	Disease 25	2,182,894	229,344	10.51	NA	NA	76,412	NA
Cambridge	Disease 26	785,338	39,670	5.05	NA	NA	32,284	NA
Cambridge	Disease 27	1,840,304	304,711	16.56	NA	NA	226,167	NA
Cambridge	Disease 28	5,050,694	1,315,276	26.04	NA	NA	748,814	NA
Cambridge	Disease 29	1,014,488	85,600	8.44	NA	NA	41,023	NA
Cambridge	Disease 30	1,205,032	23,593	1.96	NA	NA	22,036	NA
Cambridge	Disease 31	2,494,434	279,913	11.22	NA	NA	134,044	NA
Cambridge	Disease 32	807,868	9,754	1.21	NA	NA	8,814	NA
Cambridge	Disease 33	1,978,690	930,080	47.00	NA	NA	500,668	NA
Cambridge	Disease 34	2,577,566	46,319	1.80	NA	NA	42,910	NA
Cambridge	Disease 35	2,102,706	106,816	5.08	NA	NA	94,586	NA
Cambridge	Disease 36	2,815,246	438	0.02	NA	NA	434	NA
Cambridge	Disease 37	2,199,754	277,888	12.63	NA	NA	203,917	NA
Cambridge	Disease 38	2,110,646	289	0.01	NA	NA	289	NA
Cambridge	Disease 39	1,016,694	24,639	2.42	NA	NA	21,817	NA
Cambridge	Disease 40	738,246	5,724	0.78	NA	NA	5,433	NA
Cambridge	Disease 41	2,096,784	171,075	8.16	NA	NA	146,212	NA
Cambridge	Disease 42	3,247,232	2,295,486	70.69	NA	NA	813,457	NA
Cambridge	Disease 43	554,096	3,318	0.60	NA	NA	3,291	NA
Cambridge	Disease 44	1,544,178	903,730	58.52	NA	NA	452,230	NA
Cambridge	Disease 45	2,648,994	132,091	4.99	NA	NA	115,464	NA
Cambridge	Disease 46	2,091,574	112,650	5.39	NA	NA	73,381	NA
Cambridge	Disease 47	1,559,028	1,492	0.10	NA	NA	1,489	NA
Cambridge	Disease 48	2,670,292	26,551	0.99	NA	NA	25,670	NA
Cambridge	Disease 49	2,056,264	5,923	0.29	NA	NA	5,352	NA
Cambridge	Disease 50	3,119,110	81,631	2.62	NA	NA	63,264	NA
Cambridge	Disease 51	945,096	188,307	19.92	NA	NA	63,761	NA
Cambridge	Disease 52	1,047,788	21,311	2.03	NA	NA	20,805	NA
Cambridge	Disease 53	947,354	78,380	8.27	NA	NA	35,183	NA
Cambridge	Disease 54	1,729,208	736,357	42.58	NA	NA	163,249	NA
Cambridge	Disease 55	2,589,948	3,042	0.12	NA	NA	3,019	NA
Cambridge	Disease 56	631,500	19,934	3.16	NA	NA	19,197	NA
Cambridge	Disease 57	2,524,278	4,144	0.16	NA	NA	4,121	NA
Cambridge	Disease 58	1,362,442	245,797	18.04	NA	NA	87,344	NA
Cambridge	Disease 59	2,806,760	1,194,774	42.57	NA	NA	250,341	NA
Cambridge	Disease 60	2,213,584	544,664	24.61	NA	NA	170,054	NA
Cambridge	Disease 61	2,412,222	356	0.01	NA	NA	353	NA
Cambridge	Disease 62	2,639,446	41,137	1.56	NA	NA	38,139	NA
Cambridge	Disease 63	3,800,714	66,612	1.75	NA	NA	57,373	NA
Cambridge	Disease 64	4,179,442	32,927	0.79	NA	NA	30,340	NA
Cambridge	Disease 65	2,927,868	418	0.01	NA	NA	415	NA
Cambridge	Disease 66	4,635,050	592,274	12.78	NA	NA	366,585	NA
Cambridge	Disease 67	4,126,486	140,083	3.39	NA	NA	117,236	NA
Cambridge	Disease 68	2,277,294	2,755	0.12	NA	NA	2,697	NA
Cambridge	Disease 69	2,963,800	1,116,595	37.67	NA	NA	346,965	NA
Cambridge	Disease 70	1,859,700	1,163	0.06	NA	NA	1,158	NA
Cambridge	Disease 71	2,307,386	10,457	0.45	NA	NA	10,051	NA
Cambridge	Disease 72	2,041,424	8,242	0.40	NA	NA	7,926	NA
Cambridge	Disease 73	2,621,932	227,027	8.66	NA	NA	161,484	NA
Cambridge	Disease 74	2,007,874	219	0.01	NA	NA	219	NA
Cambridge	Disease 75	3,611,160	831,708	23.03	NA	NA	366,327	NA
Cambridge	Disease 76	1,596,724	1,087	0.07	NA	NA	1,079	NA
Cambridge	Disease 77	2,670,084	1,511	0.06	NA	NA	1,469	NA
Chicago	Disease 78	2,299,262	1,010	0.04	NA	NA	1,005	NA
Chicago	Disease 79	2,565,346	139	0.01	NA	NA	138	NA
Chicago	Disease 80	2,342,156	68,152	2.91	NA	NA	49,162	NA
Chicago	Disease 81	3,298,802	1,464,153	44.38	NA	NA	626,228	NA
Chicago	Disease 82	2,539,358	1,901	0.07	NA	NA	1,855	NA
Chicago	Disease 83	2,981,682	281,269	9.43	NA	NA	201,063	NA
Chicago	Disease 84	2,394,688	91,325	3.81	NA	NA	77,979	NA
Chicago	Disease 85	3,830,506	1,266,358	33.06	NA	NA	715,601	NA
Chicago	Disease 86	3,502,954	16,400	0.47	NA	NA	15,722	NA
Chicago	Disease 87	3,352,598	149,741	4.47	NA	NA	73,399	NA
Chicago	Disease 88	2,929,918	331,619	11.32	NA	NA	252,323	NA
Chicago	Disease 89	3,473,508	1,074,750	30.94	NA	NA	509,394	NA
Chicago	Disease 90	1,214,702	3,317	0.27	NA	NA	3,220	NA
Chicago	Disease 91	3,825,838	21,981	0.57	NA	NA	20,243	NA
Chicago	Disease 92	2,431,028	388,718	15.99	NA	NA	110,424	NA
Chicago	Disease 93	2,125,146	248,822	11.71	NA	NA	131,995	NA
Chicago	Disease 94	2,879,428	469,166	16.29	NA	NA	115,545	NA
Chicago	Disease 95	2,267,290	270,505	11.93	NA	NA	63,267	NA
Chicago	Disease 96	2,804,470	579,565	20.67	NA	NA	187,402	NA
Chicago	Disease 97	3,202,992	184,491	5.76	NA	NA	64,034	NA
Chicago	Disease 98	2,759,690	24,435	0.89	NA	NA	23,751	NA
Chicago	Disease 99	1,092,508	6,756	0.62	NA	NA	6,499	NA
Chicago	Disease 100	3,637,688	328,733	9.04	NA	NA	141,947	NA
Chicago	Disease 101	3,119,986	396,859	12.72	NA	NA	183,655	NA
Chicago	Disease 102	2,732,006	1,316,100	48.17	NA	NA	522,713	NA

Initially, total reads (unduplicated) were mapped to ALL contigs. In healthy individuals, all reads were deduplicated and then mapped to our contigs. Because deduplication did not modify our results, in disease individuals only used reads (reads that mapped to our contigs initially) were further trimmed, deduplicated, and remapped.

^{^†}

Individuals from this dataset were not analyzed separately.