Supplemental Digital Content 2. Sequence statistics for the bacterial 16S rRNA gene and viral metagenomic analyses, before and after processing.
(A) Newly-processed samples. Bacterial replicates and DNA/RNA viral reads are shown separately.
Raw 454 reads
1st; 2nd replicate
Bacterial hits
1st; 2nd replicate
Raw 454 reads
DNA; RNA
Viral hits
DNA; RNA
Num samples: 41; 41 41; 41 41; 39 41; 24
Total count: 455,440; 259,166 264,287; 223,830 1,094,027; 498,709 196,098; 5971 Counts/sample
summary:
Min: 1,501; 892 987; 770 1,575; 0 1; 0
Max: 23,918; 16,221 14,711; 13,000 56,319; 55,562 24,698; 3,088
Median: 9,626; 6,660 5,845; 5,723 27,342; 8,337 1,974; 1
Mean: 11,108; 6,321 6,446; 5,459 26,683; 12,163 4782; 145 Std. dev.: 5,475; 3,008 2,933; 2,440 11,279; 12,814 5881; 523 Counts/sample detail:
Ctrl01 9,299; 7,548 5,220; 6,394 27,342; 55,562 1,974; 1
Ctrl02 9,375; 6,628 5,450; 5,348 25,846; 27,880 12,937; 358
Ctrl03 10,376; 6,996 5,845; 5,752 28,436; 3,189 18,702; 0
Ctrl04 13,676; 16,221 5,734; 13,000 17,556; 13,183 589; 48
Ctrl05 9,402; 8,015 4,828; 5,485 23,149; 17,214 2,937; 6
Ctrl06 8,453; 7,265 5,939; 6,217 11,192; 6,132 1,462; 179
Ctrl07 9,058; 8,049 5,079; 6,797 33,365; 1,670 7,799; 1
Ctrl08 8,618; 6,837 5,487; 5,834 15,060; 4,955 4,711; 5
Ctrl09 8,166; 8,826 4,726; 7,188 44,268; 365 11,312; 0
Ctrl10 8,156; 6,705 4,920; 5,836 12,672; 7,357 1,504; 0
Ctrl11 9,678; 6,146 6,723; 5,196 1,575; 28,335 262; 114
Ctrl12 9,626; 9,355 6,193; 7,309 11,692; 80 1,481; 1
CD01F.b 19,296; 6,555 9,859; 6,212 21,033; 6,811 14,062; 0
CD02F.b 9,105; 3,676 4,420; 3,393 31,809; 0 14,362; 0
CD03B.a 7,571; 5,018 6,311; 4,492 10,291; 17,390 1,465; 1
CD03BA.c 1,501; 892 987; 770 32,933; 9,641 110; 3
CD03BNA.c 2,946; 1,876 2,274; 1,672 31,492; 523 907; 0
CD03F.a 12,650; 4,957 7,453; 4,363 38,080; 13,489 11,519; 0 CD03F.c 18,131; 6,660 9,908; 5,996 33,718; 25,693 8,269; 23
CD04B.a 5,187; 3,306 3,364; 2,900 18,171; 549 1,829; 0
CD04F.a 23,918; 9,071 12,158; 8,131 26,677; 3,542 2,872; 1,362
CD05B.a 4,113; 2,526 3,025; 2,352 29,417; 23,878 266; 28
CD05BA.c 3,342; 2,235 2,417; 1,994 40,977; 10,781 1; 1
CD05BNA.c 2,130; 1,375 1,694; 1,268 22,752; 8,337 8; 0
CD05F.a 9,596; 3,692 3,869; 3,457 24,395; 4,876 2,141; 0
CD05F.c 9,598; 3,492 5,713; 3,249 29,658; 7,489 2,095; 3,088
CD06B.a 10,168; 6,710 8,072; 6,210 17,961; 11,903 585; 2
CD06F.a 12,975; 4,126 5,947; 3,640 42,860; 15,750 11,684; 277
CD07B.a 14,395; 9,433 10,613; 7,543 24,161; 1,381 5,002; 0
CD07F.a 21,259; 8,002 10,296; 7,285 21,510; 10,284 1,271; 0
CD08B.a 9,094; 6,066 7,216; 5,566 16,500; 0 1,527; 0
CD08F.a 22,952; 8,429 12,510; 7,767 45,563; 18,958 2,622; 25 CD09B.a 8,917; 6,100 7,169; 5,612 56,319; 26,715 24,698; 10
CD09F.a 11,093; 4,142 5,796; 3,845 29,274; 2,578 3,205; 17
CD10BA.c 22,706; 13,962 14,711; 11,816 31,748; 92 358; 0
CD10BNA.c 11,417; 7,238 7,046; 5,723 30,402; 50,254 9,936; 0
CD10F.c 13,504; 4,766 5,591; 4,116 28,771; 22,973 1,275; 0
CD11BA.c 10,691; 6,932 8,358; 6,411 33,741; 6,442 27; 1
CD11BNA.c 11,861; 7,545 9,081; 6,698 16,870; 20,894 1; 1
CD11F.c 14,137; 5,032 5,676; 4,607 12,907; 11,263 7,076; 419
CD12F.c 17,304; 6,761 6,609; 6,386 41,884; 301 1,255; 0
(B) All samples*.Bacterial replicates and DNA/RNA viral reads are shown joined.
Raw 454 reads Bacterial hits Raw 454 reads Viral hits
Num samples: 57 57 57 57
Total count: 843,540 572,493 2,152,590 381,354
Counts/sample summary:
Min: 2,393 1,757 11,772 2
Max: 36,668 26,527 83,034 32,269
Median: 15,017 10,283 31,852 2,869
Mean: 14,799 10,043 37,764 6,690
Std. dev.: 7,705 5,167 17,799 7,694
Counts/sample detail:
V1* 10,117 6,273 12,480 3,744
V2* 8,832 5,927 28,292 3,471
V3* 5,502 3,229 16,877 3,137
V4* 10,125 6,658 32,269 718
V5* 8,205 5,014 18,556 784
V6* 12,110 7,892 18,620 1,519
V7* 9,031 5,945 12,707 4,063
V8* 9,935 5,988 16,595 786
Ctrl01 16,847 11,614 82,904 1,975
Ctrl02 16,003 10,798 53,726 13,295
Ctrl03 17,372 11,597 31,625 18,702
Ctrl04 29,897 18,734 30,739 637
Ctrl05 17,417 10,313 40,363 2,943
Ctrl06 15,718 12,156 17,324 1,641
Ctrl07 17,107 11,876 35,035 7,800
Ctrl08 15,455 11,321 20,015 4,716
Ctrl09 16,992 11,914 44,633 11,312
Ctrl10 14,861 10,756 20,029 1,504
Ctrl11 15,824 11,919 29,910 376
Ctrl12 18,981 13,502 11,772 1,482
C2* 7,803 4,268 53,420 2,496
C3* 8,048 5,334 43,543 1,709
C4* 8,241 4,862 67,822 2,869
C5* 5,616 3,535 52,747 4,417
C6* 9,970 6,310 54,838 2,438
C7* 5,232 2,754 39,990 2,559
C8* 6,968 4,702 62,063 5,322
C10* 9,278 5,685 29,035 1,079
CD01F.b 25,851 16,071 27,844 14,062
CD02F.b 12,781 7,813 31,809 14,362
CD03B.a 12,589 10,803 27,681 1,466
CD03BA.c 2,393 1,757 42,574 113
CD03BNA.c 4,822 3,946 32,015 907
CD03F.a 17,607 11,816 51,569 11,519
CD03F.c 24,791 15,904 59,411 8,292
CD04B.a 8,493 6,264 18,720 1,829
CD04F.a 32,989 20,289 30,219 4,234
CD05B.a 6,639 5,377 53,295 294
CD05BA.c 5,577 4,411 51,758 2
CD05BNA.c 3,505 2,962 31,089 8
CD05F.a 13,288 7,326 29,271 2,141
CD05F.c 13,090 8,962 37,147 5,183
CD06B.a 13,090 14,282 29,864 587
CD06F.a 16,878 9,587 58,610 11,961
CD07B.a 17,101 18,156 25,542 5,002
CD07F.a 23,828 17,581 31,794 1,271
CD08B.a 29,261 12,782 16,500 1,527
CD08F.a 15,160 20,277 64,521 2,647
CD09B.a 31,381 12,781 83,034 24,708
CD09F.a 15,017 9,641 31,852 3,222
CD10BA.c 15,235 26,527 31,840 358
CD10BNA.c 36,668 12,769 80,656 9,936
CD10F.c 18,655 9,707 51,744 1,275
CD11BA.c 18,270 14,769 40,183 28
CD11BNA.c 17,623 15,779 37,764 2
CD11F.c 19,406 10,283 24,170 7,495
CD12F.c 24,065 12,995 42,185 1,255
* Samples from previous study (Pérez-Brocal et al, 2013) included in the present one.
