Research Article
Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt
Table 1
Sequence analysis for the generated reads and the remaining reads after preprocessing, filtration, preclustering, and chimeras removal.
| Sample code | Total reads | Reads passing quality filtering | Number of unique reads | Total number of reads before preclustering | Total number of reads after preclustering | Number of chimeras | Number of reads after chimeras removal | Percentage of chimeras sequence |
| 1 | 130378 | 102374 | 69001 | 52390 | 22726 | 4334 | 18392 | 19.10% | 2 | 99713 | 78230 | 52970 | 43726 | 20319 | 6216 | 14103 | 30.60% | 3 | 148927 | 117143 | 83994 | 65789 | 30793 | 7323 | 23470 | 23.80% | 4 | 136015 | 107981 | 73508 | 52409 | 24382 | 5070 | 19312 | 20.80% | 5 | 91410 | 72590 | 54671 | 43282 | 22740 | 4037 | 18702 | 17.80% | 6 | 159563 | 124396 | 81290 | 65593 | 29018 | 7503 | 21515 | 25.90% | 7 | 179597 | 140847 | 94637 | 72983 | 32522 | 6942 | 25580 | 21.30% | 8 | 153991 | 121551 | 76195 | 59673 | 26540 | 8457 | 18083 | 31.90% | 9 | 140290 | 108819 | 77616 | 59922 | 27164 | 5045 | 22119 | 18.60% | 10 | 93517 | 75671 | 50873 | 40472 | 17933 | 4568 | 13365 | 25.50% | 11 | 153126 | 120768 | 91730 | 75798 | 41305 | 18169 | 23136 | 44% | 12 | 159655 | 129432 | 95261 | 67017 | 31948 | 6394 | 25554 | 20% | 13 | 72461 | 57647 | 40291 | 32138 | 16499 | 5210 | 11289 | 31.60% | 14 | 98370 | 77375 | 56593 | 46254 | 22690 | 5828 | 16862 | 25.70% | 15 | 126414 | 99959 | 65761 | 52345 | 24373 | 7679 | 16694 | 31.50% | 16 | 128433 | 101274 | 65627 | 52214 | 24255 | 9275 | 14980 | 38.20% | 17 | 202643 | 155799 | 107509 | 84438 | 42083 | 18983 | 23100 | 45.10% | 18 | 183073 | 144386 | 96114 | 73998 | 33752 | 8485 | 25267 | 25.10% | 20 | 188766 | 147582 | 107487 | 84994 | 41383 | 9505 | 31878 | 23% | Average | 139281.2 | 109674.9 | 75848.84 | 59233.42 | 28022.37 | 7843.32 | 20179 | 27% |
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