Table 2.
Characteristics of lake and marine metagenomes
| ID | Reference/site | Size after QC (Mb) | Reads after QC | GC content (%) | Isoelectric point | SSU rRNA genes | % Eukaryotic SSU rRNA genes | Reads with STRING hit | Reads with COG assignment | % Reads with COG assignment | Average number of single copy COGs | % Bacteria among single copy COGs | Simple EGS Mb/single copy COG |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DamariscottaSP | Martinez-Garcia et al. 2012 | 121 | 281 625 | 48.6 | 9.75 | 531 (185/0/5) | 2.6 | 149 906 | 135 640 | 42 | 78 | 94 | 1.55 |
| DamariscottaSU | Martinez-Garcia et al. 2012 | 140 | 323 939 | 48.2 | 9.82 | 666 (200/0/27) | 11.9 | 156 281 | 140 701 | 50 | 93 | 93 | 1.51 |
| Ekoln | this study | 115 | 284 609 | 46.0 | 9.49 | 622 (209/0/13) | 5.9 | 107 593 | 94 783 | 33 | 69 | 95 | 1.67 |
| Erken | this study | 233 | 554 862 | 44.9 | 9.41 | 1170 (399/0/5) | 1.2 | 273 058 | 250 931 | 45 | 196 | 93 | 1.19 |
| Lanier | Oh et al. 2011 | 449 | 1 078 031 | 47.1 | 9.77 | 1989 (714/0/20) | 2.7 | 440 459 | 399 647 | 37 | 252 | 93 | 1.78 |
| MendotaSP | Martinez-Garcia et al. 2012 | 133 | 319 321 | 45.7 | 9.52 | 1118 (242/0/149) | 38.1 | 124 837 | 111 654 | 25 | 77 | 97 | 1.73 |
| MendotaSU | Martinez-Garcia et al. 2012 | 192 | 447 054 | 47.7 | 9.75 | 795 (247/0/31) | 11.2 | 173 517 | 146 222 | 46 | 76 | 95 | 2.53 |
| Spark | Martinez-Garcia et al. 2012 | 26 | 66 160 | 52.5 | 10.01 | 108 (28/0/5) | 15.2 | 22 364 | 19 857 | 30 | 8 | 87 | 3.25 |
| Trout | Martinez-Garcia et al. 2012 | 60 | 150 515 | 46.5 | 9.59 | 335 (63/0/21) | 25.0 | 46 795 | 41 628 | 28 | 26 | 88 | 2.31 |
| Vattern | this study | 117 | 285 637 | 47.4 | 9.67 | 540 (177/0/15) | 7.8 | 116 970 | 103 047 | 36 | 66 | 93 | 1.77 |
| Yellowstone1 | SRR077348 | 181 | 416 139 | 43.7 | 9.34 | 541 (212/0/2) | 0.9 | 152 376 | 136 972 | 33 | 83 | 93 | 2.18 |
| Yellowstone2 | SRR078855 | 107 | 346 239 | 41.4 | 9.03 | 754 (256/1/0) | 0.0 | 91 459 | 86 132 | 25 | 75 | 97 | 1.43 |
| FRESHWATER (Mean) | 156 | 379 511 | 46.6 | 9.60 | 764 (244/0/24) | 10.2 | 154 635 | 138 935 | 37 | 92 | 93 | 1.91 | |
| BATS0 | Sargasso Sea | 118 | 478 976 | 48.0 | 9.74 | 1137 (431/0/13) | 2.9 | 142 979 | 131 449 | 27 | 104 | 97 | 1.14 |
| BATS200 | Sargasso Sea | 134 | 525 891 | 48.3 | 9.70 | 1049 (310/38/13) | 3.6 | 133 259 | 121 763 | 23 | 97 | 85 | 1.38 |
| BATS250 | Sargasso Sea | 115 | 456 677 | 46.6 | 9.63 | 606 (183/20/9) | 4.2 | 95 919 | 88 658 | 19 | 70 | 89 | 1.65 |
| BATS40 | Sargasso Sea | 95 | 394 461 | 48.1 | 9.78 | 675 (227/0/17) | 7.0 | 86 262 | 79 155 | 20 | 67 | 96 | 1.42 |
| EqDP35155 | Equatorial Pacific | 56 | 219 390 | 45.4 | 9.70 | 508 (164/10/3) | 1.7 | 62 135 | 57 103 | 26 | 53 | 91 | 1.05 |
| NPTG35179 | North Pacific Tropical Gyre | 45 | 181 907 | 44.8 | 9.53 | 656 (253/4/4) | 1.5 | 55 589 | 51 145 | 28 | 45 | 95 | 1.00 |
| PNEq35163 | Pacific North Equatorial | 55 | 221 925 | 49.8 | 9.94 | 790 (300/6/5) | 1.6 | 59 337 | 53 915 | 24 | 52 | 92 | 1.06 |
| PNEqCc35171 | Pacific North Equatorial | 13 | 50 267 | 42.5 | 9.38 | 101 (31/3/2) | 5.6 | 15 791 | 14 620 | 29 | 13 | 92 | 0.97 |
| SPSG35131 | South Pacific Subtropical Gyre | 36 | 155 219 | 47.7 | 9.77 | 583 (225/1/4) | 1.7 | 46 502 | 42 726 | 28 | 39 | 96 | 0.94 |
| SPSG35139 | South Pacific Subtropical Gyre | 16 | 61 766 | 41.9 | 9.33 | 169 (71/1/0) | 0.0 | 23 083 | 21 352 | 35 | 19 | 97 | 0.85 |
| SPSG35147 | South Pacific Subtropical Gyre | 21 | 80 088 | 43.2 | 9.47 | 259 (97/3/1) | 1.0 | 28 681 | 26 504 | 33 | 25 | 93 | 0.83 |
| WChannelApr | Gilbert et al. 2010 | 102 | 278 931 | 39.2 | 9.01 | 317 (64/0/6) | 8.6 | 82 819 | 67 968 | 24 | 35 | 90 | 2.91 |
| WChannelJan | Gilbert et al. 2010 | 208 | 548 680 | 38.4 | 8.97 | 724 (195/17/6) | 2.8 | 180 844 | 153 475 | 28 | 100 | 74 | 2.08 |
| MARINE (Mean) | 78 | 281 091 | 44.9 | 9.53 | 583 (196/8/6) | 3.2 | 77 938 | 69 987 | 25 | 55 | 91 | 1.33 |
The isoelectric point represents the average pH at which predicted genes from a specific metagenome carry no electric charge. In column seven, numbers in parentheses represent the number of SSU rRNA genes annotated to Bacteria, Archaea and Eukaryota, respectively.
COG, clusters of orthologous groups; EGS, effective genome size; QC, quality filtering; mb, megabases; SSU rRNA, small subunit of the ribosomal RNA.