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Table 1 Amplication and mapping metrics for samples with respiratory viruses detected by RNA-seq and/or by qPCR. Detected virus coverage was scaled by the total number of raw reads divided by 10e6. If the closest reference differed between the multiple contigs for a sample, then the most frequent closest reference sequence was reported. In all cases the closest reference for all contigs of a sample were of the same viral species (i.e., no dual infections were detected)

From: Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome

Subject qPCR RNA-seq mapping metrics Detected virus
Virus Gene Total reads Resp. virus reads % Viral reads Species Strain/serotype Closest reference (NCBI acc) Virus mapped to NCBI reference Coverage (scaled)
Species Ct CCL8 CXCL11
Asthma-1 None NA 8426.9 109,137.3 10,720,551 164,870 1.54 HPIV 4a KF483663.1 98.9% 1271.6x
Control-1 HRV 29.36 7.7 190.8 9,818,450 74,935 0.763 HEV C105 JX393302.1 92.8% 1259.7x
Asthma-2 RSV 20.05 4356.0 103,107.1 11,597,132 58,263 0.502 RSV A KJ672478.1 99.8% 473.5x
Control-2 HPIV1 24.37 749.7 13,819.3 14,029,017 26,045 0.186 HPIV 1 KF687314.1 99.8% 172.2x
Control-3 HRV 24.19 170.7 4377.0 10,591,814 4081 0.039 HRV A55 DQ473511.1 80.8% 66.9x
Asthma-3 HPIV1 25.29 3148.7 13,129.6 9,738,089 6648 0.068 HPIV 1 KF530212.1 99.8% 64.4x
Control-4 HRV 25.86 7042.3 89,477.7 16,450,743 2878 0.017 HRV A59 JN541266.1 99.3% 37.9x
Asthma-4 HRV 38.15 6.4 68.5 15,103,156 829 0.005 HRV C JF317015.1 99.9% 11.7x
Control-5 None NA 1430.1 24,191.0 14,863,334 2671 0.018 Influenza B CY171998.1 5.7% 7.8x
Control-6 HRV 30.24 67.3 734.7 9,732,129 203 0.002 HRV A59 JN541266.1 99.5% 4.5x
Asthma-5 HRV 29.17 90.1 1010.9 8,269,118 156 0.002 HRV A100 FJ445175.1 91.0% 3.6x
Control-7 None NA 4.7 166.0 10,579,380 780 0.007 HCoV OC43 KF530099.1 95.0% 3.2x
Asthma-6 HRV 28.60 1780.1 89,078.1 9,944,802 97 0.001 HRV A55 DQ473511.1 85.6% 1.7x
Control-8 HMPV 30.78 10.7 146.7 9,978,447 107 0.001 HMPV A2 GQ153651.1 99.1% 1.2x
Control-9 HRV 40.98 0.7 28.6 14,107,522 76 0.0005 HRV C JF317015.1 100% 1.2x
Control-10 HRV 44.08 1.3 58.1 14,005,041 39 0.0003 HEV CY135 KF322116.1 15.4% 0.7x
Control-11 HRV 33.35 1.0 20.2 15,787,336 35 0.0002 RSV A EF155421.1 100% 0.5x
Control-12 None NA 0.5 76.5 10,880,596 24 0.0002 RSV A KJ672484.1 100% 0.2x
Asthma-7 HRV 37.60 2.6 90.8 16,883,056 9 5.33e-05 HCoV NA* JX504050.1 66.7% NA*
Asthma-8 RSV 35.95 3.6 145.9 15,782,330 7 4.44e-05 RSV NA* KJ672484.1 85.7% NA*
Asthma-9 HRV 42.14 2.1 132.1 13,910,896 5 3.59e-05 HRV NA* KC342104.1 40% NA*
Control-13 HRV 33.51 1.7 37.8 17,449,199 4 2.29e-05 HRV NA* AB904651.1 25% NA*
Control-14 HRV 37.76 0.8 5.3 14,074,760 0 0 NA NA NA NA NA
Asthma-10 RSV/HPIV1 40.04/37.25 3.2 95.6 15,013,585 0 0 NA NA NA NA NA
Control-15 RSV 37.8 4.9 443.7 17,496,674 0 0 NA NA NA NA NA
  1. *Too few reads to perform assembly into contigs
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Genome Biology

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