From: In silico analyses of metagenomes from human atherosclerotic plaque samples
Patients | Platform | Sample ID-DNA | Raw reads | Non-Hg19 reads | Non-Hg19 (%) | RapSearch processed (as in MEGAN) | Assigned in MEGAN (MSc:50 MSp25 MinCompl:0.44 and paired protocol) | Bacteria | % Bacteria |
---|---|---|---|---|---|---|---|---|---|
Cases | Hiseq 2000 | 48 | 93,124,682 | 31,504,036 | 33.83 | 8,404,029 | 3,763,197 | 243,336 | 2.90Â % |
Hiseq 2000 | 49 | 101,840,018 | 53,068,718 | 52.11 | 12,405,108 | 6,772,304 | 436,463 | 3.52Â % | |
Hiseq 2000 | 50 | 94,765,328 | 43,109,046 | 45.49 | 11,643,905 | 6,419,975 | 505,239 | 4.34Â % | |
Hiseq 2000 | 51 | 112,426,390 | 50,653,838 | 45.06 | 10,711,699 | 4,899,567 | 216,511 | 2.02Â % | |
Hiseq 2000 | 52 | 88,328,470 | 36,795,952 | 41.66 | 10,574,678 | 5,766,665 | 492,013 | 4.65Â % | |
Hiseq 2000 | 53 | 124,000,764 | 41,858,084 | 33.76 | 10,057,354 | 4,676,002 | 243,775 | 2.42Â % | |
Hiseq 2000 | 54 | 93,124,682 | 82,366,266 | 88.45 | 19,199,623 | 9,229,157 | 365,993 | 1.91Â % | |
Hiseq 2000 | 237 | 141,334,092 | 58,853,792 | 41.64 | 6,946,473 | 3,854,397 | 249,369 | 3.59Â % | |
Hiseq 2000 | 238 | 153,302,968 | 36,976,828 | 24.12 | 5,216,154 | 3,002,923 | 835,412 | 16.02Â % | |
Hiseq 2000 | 239 | 154,652,444 | 48,177,200 | 31.15 | 5,643,923 | 3,045,461 | 222,363 | 3.94Â % | |
Hiseq 2000 | 240 | 101,591,496 | 46,000,276 | 45.28 | 5,166,877 | 2,640,033 | 110,186 | 2.13Â % | |
Hiseq 2000 | 241 | 99,927,824 | 42,032,952 | 42.06 | 4,607,355 | 2,471,259 | 153,425 | 3.33Â % | |
Hiseq 2000 | 242 | 82,850,664 | 46,721,284 | 56.39 | 5,002,916 | 2,716,756 | 135,617 | 2.71Â % | |
Hiseq 2000 | 243 | 104,094,892 | 52,853,464 | 50.77 | 5,726,930 | 3,095,542 | 193,819 | 3.38Â % | |
Hiseq 2500 | 977 (P0613) | 111,699,176 | 13,191,406 | 11.81 | 2,344,220 | 955,602 | 74,646 | 3.18Â % | |
Miseq V1 | P0613 repeat | 7,184,184 | 980,004 | 13.64 | 759,262 | 228,262 | 31,889 | 4.20Â % | |
 | 977 + APD1 | 118,883,360 | 14,171,410 | 11.92 | 3,103,482 | 1,183,864 | 106,535 | 3.43 % | |
Controls | Hiseq 2000 | 55 | 105,779,932 | 29,019,712 | 27.43 | 8,911,853 | 4,040,359 | 293,160 | 3.29Â % |
Hiseq 2000 | 56 | 128,471,814 | 10,767,822 | 8.38 | 4,680,735 | 1,922,688 | 204,397 | 4.37Â % | |
Hiseq 2000 | 232 | 127,173,774 | 25,793,632 | 20.72 | 3,267,969 | 1,726,714 | 164,711 | 5.04Â % | |
Hiseq 2000 | 233 | 166,547,592 | 29,282,304 | 17.58 | 4,559,468 | 2,634,338 | 649,226 | 14.24Â % | |
Hiseq 2000 | 234 | 114,673,124 | 37,683,568 | 32.86 | 4,550,457 | 2,477,740 | 193,659 | 4.26Â % | |
Hiseq 2000 | 235 | 151,195,284 | 34,767,160 | 22.99 | 4,633,661 | 2,550,975 | 231,926 | 5.01Â % | |
Hiseq 2000 | 236 | 152,179,180 | 32,269,700 | 21.21 | 4,254,572 | 2,319,403 | 204,778 | 4.81Â % | |
Total | Â | Â | 2,610,268,774 | 685,143,146 | 26.25 | Â | Â | Â | 4.60Â % |