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Table 1 Number of reads reported from sequencing a multiplexed viral pathogen reagent

From: Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples

  Replicate 1 Replicate 2
Virus species (most frequent strain) All 3,505,318 reads 2,000,000 reads 150,000 reads All 2,676,604 reads 2,000,000 reads 150,000 reads
25 target viruses
 Human astrovirus (Human astrovirus 1) 27,622 15,783.2 1184.1 8040.6 596.2 8040.6
 Enterovirus B (Human coxsackievirus B4) 27,252 15,539.0 1161.3 22,707.3 1704.4 22,707.3
 Human herpesvirus 1 67 39.0 3.5 81.4 5.5 81.4
 Human herpesvirus 2 2 1.3 0.4 7.0 0.4 7.0
 Human herpesvirus 3 (Human herpesvirus 3 strain Dumas) 34 17.4 1.4 84.2 6.4 84.2
 Human herpesvirus 4 166 98.1 8.2 104.7 8.7 104.7
 Human herpesvirus 5 8327 4743.1 352.1 7028.5 524.4 7028.5
 Human mastadenovirus C (Human adenovirus 2) 23 11.5 0.8 299.1 19.6 299.1
 Human mastadenovirus F (Human adenovirus 41) 2 2.0 0.0 13.9 1.7 13.9
 Human metapneumovirus 0 0.0 0.0 0.0 0.0 0.0
 Human parainfluenza virus 1 21,387 12,170.8 921.2 9601.2 718.6 9601.2
 Human parainfluenza virus 2 2879 1651.5 119.6 33.1 1.6 33.1
 Human parainfluenza virus 3 0 0.0 0.0 0.0 0.0 0.0
 Human parainfluenza virus 4 (Human parainfluenzavirus 4b) 21,858 12,478.6 924.3 10,089.8 760.2 10,089.8
 Human respiratory syncytial virus 0 0.0 0.0 229.4 15.5 229.4
 Human Rhinovirus A (Human rhinovirus A39) 0 0.0 0.0 2238.4 158.6 2238.4
 Influenzavirus A H1N1 0 0.0 0.0 0.0 0.0 0.0
 Parechovirus A (Human parechovirus 3) 1,492,756 851,560.6 63,862.7 565,228.5 42,434.5 565,228.5
 Rotavirus A 6 2.8 0.3 8.5 0.8 8.5
 Sapporovirus (Sapovirus Hu/GI.2/BR-DF01/BRA/2009 and Hu/G1/BE-HPI01/DE/2012) 1019 575.5 45.2 62.8 5.1 62.8
 Human coronavirus 229E 0 0.0 0.0 0.0 0.0 0.0
 Norovirus GI 0 0.0 0.0 0.0 0.0 0.0
 Norovirus GII 0 0.0 0.0 0.0 0.0 0.0
 Influenza virus B 0 0.0 0.0 0.0 0.0 0.0
 Influenza virus A H3N2 0 0.0 0.0 0.0 0.0 0.0
Non-target viruses
 Bovine viral diarrhea virus 1 1446 820.6 63.6 1891.8 140.3 1891.8
 Bovine viral diarrhea virus 2 1 0.4 0.4 0.0 0.0 0.0
 Primate bocaparvovirus 1 0 0.0 0.0 0.0 0.0 0.0
 Primate bocaparvovirus 2 208 118.2 7.5 91.6 6.8 91.6
 Human enterovirus (Enterovirus CA55–1988) 3199 1834.7 140.6 380.6 28.7 380.6
 Aichi virus 0 0.0 0.0 0.0 0.0 0.0
 Ungulate bocaparvovirus 1 0 0.0 0.0 0.0 0.0 0.0
 Porcine/other circovirus 0 0.0 0.0 0.0 0.0 0.0
Total virus reads 1,608,254 917,448.3 68,797.2 840,888 628,222.4 47,138.0
Number of detected target viruses 15 14.4 11.7 17 17.0 15.7
  1. For subsamples of reads, the average number of virus reads and detected target viruses in 10 random samplings is shown
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Microbiome

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