see countAmplicons.R for script to turn BCLs and XLSX description of experiment into tables of counts per amplicon
see analysis for run-specific analysis scripts
see runs for BCLs, gzipped fastqs and tables of amplicon counts for each experiment
Statistics and notes for each sequencing run:
| Run | Instrument | Notes | % PhiX Observed | % PhiX Targeted | Conc. Loaded (pM) | Cluster Density | Cluster PF (%) |
|---|---|---|---|---|---|---|---|
| v40 | NextSeqM | - | 69 | 70 | 1.5 pM | 93K/mm2 | 94%PF |
| v39 | NextSeqH | - | 0.4 | 50 | 1.8pM | 126K/mm2 | 42%PF |
| Run | Instrument | Notes | % PhiX Observed | % PhiX Targeted | Conc. Loaded (pM) | RT | Indexing Strategy | PCR cycles | Read | Cluster PF (%) | % ≥Q30 | Yield | Error Rate% | Reads PF | Density | Tiles | Legacy Phas/Prephas (%) | Intensity |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| v38 | MiSeq | - | ||||||||||||||||
| v37 | MiSeq | NS 1:5 | 29.90 | 35 | 25 | Taqpath | - | 50 | 1 | 80.96 ±6.08 | 96.03 | 559.02Mbp | 0.35±0.32 | 22,360,804 | 1,135±60 | 38 | 0.002/0.002 | 181±20 |
| v36 | MiSeq | NS 1:4 and 1:5 | 21.26 | 35 | 25 | Taqpath | - | 50 | 1 | 88.05±3.46 | 96.10 | 614.70Mbp | 0.21±0.08 | 24,588,136 | 1,118±29 | 38 | 0.005/0.000 | 149±25 |
| v35 | MiSeq | ED | 26.89 | 35 | 25 | Taqpath | - | 50 | 1 | 89.50±2.29 | 96.79 | 638.27Mbp | 0.21±0.18 | 25,530,596 | 1,133±27 | 38 | 0.000/0.000 | 156±20 |
| v34 | MiSeq | ED | 31.96 | 35 | 25 | Taqpath | - | 50 | 1 | 90.38±1.97 | 96.92 | 602.46Mbp | 0.26±0.34 | 24,098,420 | 1,060±29 | 38 | 0.000/0.000 | 170±27 |
| v33 | MiSeq | - | 33.65 | 35 | 25 | Taqpath | - | 50 | 1 | 89.05 ±1.85 | 96.78 | 637.94Mbp | 0.16±0.02 | 25,517,552 | 1,146±15 | 38 | 0.001/0.000 | 175±26 |
| v32 | MiSeq | - | 35.56 | 35 | 25 | Taqpath | - | 50 | 1 | 92.27±1.46 | 97.46 | 539.25Mbp | 0.23±0.05 | 21,570,046 | 924±14 | 38 | 0.000 / 0.002 | 195±31 |
| v31 | MiSeq | - | 34.78 | 35 | 25 | Taqpath | - | 50 | 1 | 90.15±3.09 | 96.87 | 564.97Mbp | 0.17±0.04 | 22,598,764 | 996±21 | 38 | 0.004/0.001 | 176±11 |
| v30 | MiSeq | Saliva TBE .5X Tw20; 95C 30 min; Ashe; ED; | 30.38 | 35 | 25 | Taqpath | Semi-Combinatorial | 50 | 1 | 92.63±1.25 | 97.49 | 487.05Mbp | 0.31±0.07 | 19,482,174 | 815±32 | 38 | 0.000/0.000 | 164 ±22 |
| v29 | MiSeq | Saliva TBE .5X Tw20; 95C 30 min; Ashe; ED; | 27.5 | 35 | 25 | Taqpath | Semi-Combinatorial | 50 | 1 | 92.86±1.38 | 97.84 | 624.03Mbp | 0.20±0.02 | 24,961,348 | 1,057±25 | 38 | 0.000/0.000 | 198 ±28 |
| v28 | MiSeq | Saliva TBE .5X Tw20; 95C 30 min; Ashe; ED; | 41 | 35 | 25 | Taqpath | Semi-Combinatorial | 50 | 1 | 90.11±2.04 | 97.21 | 629.71Mbp | 0.18±0.34 | 25,188,428 | 1,117±14 | 38 | 0.000/0.000 | 180±25 |
| v27 | MiSeq | Saliva TE,RNASecure,Qiagen Protease + 95C heating; ATCC after heat; ED; Ashe 2x TBE w/ 0.5% Tw20 7uL | 18 | 30 | 25 | Taqpath | UDI | 50 | 1 | 94.15±1.28 | 98.01 | 556.26Mbp | 0.22±0.04 | 22,250,444 | 923±23 | 38 | 0.009/0.000 | 208±31 |
| v26 | MiSeq | Saliva TE/RNASecQP; 2X TBE; TBE + Tween ; VTM +95C heat before or after adding ATCC; ED | 44 | 40 | 25 | Taqpath | Semi-Combinatorial | 50 | 1 | 93.29±1.14 | 97.87 | 550.14Mbp | 0.15±0.02 | 22,005,736 | 921±16 | 38 | 0.004/0.007 | 186±29 |
| v25 | MiSeq | Saliva TBE+/tween; TE,RNASecure,Qiagen Protease; +/- 95 C heating | 36 | 40 | 25 | Taqpath | UDI | 50 | ||||||||||
| v24 | MiSeq | Saliva +/- RNA Secure; NP in VTM, NS, or Amies; dilutions in water | 42 | 40 | 25 | Taqpath | Semi-Combinatorial | 50 | 1 | 92.85±1.17 | 97.79 | 483.40Mbp | 0.14±0.04 | 19,336,026 | 829±18 | 38 | 0.014/0.040 | 183 ±28 |
| v23 | MiSeq | NP in VTM diluted; eSwab(aimes); Saliva in cells2cdna; NP in NS diluted; increased lysate vol to 10uL; dilutions in TE | 37 | 40 | 26 | Taqpath | UDI | 50 | 1 | 92.69±0.86 | 97.88 | 570.91Mbp | 0.14±0.03 | 22,836,378 | 971±15 | 38 | 0.000/0.000 | 185 ±26 |
| v22 | MiSeq | Saliva undiluted; NP into VTM +/- dilution; v14 rerun; | 15 | 40 | 25 | Taqpath | Semi-Combinatorial | 40 and 50 | 1 | 96.35±0.88 | 98.57 | 347.74Mbp | 0.20±0.31 | 13,909,713 | 560±20 | 38 | 0.135/0.107 | 195±34 |
| v21 | NextSeq | NextSeq; mix of v18,v19,v20 | 8 | 35 | 1.5 | Taqpath | UDI | 40 | 1 | 95.54±0.45 | 98.48 | 0.17Gbp | 0.36±0.10 | 27,807,589 | 33±1 | 72 | 0.119/0.183 | 12741±809 |
| v20 | MiSeq | EUA (LoD confirmation); Saliva undiluted | 11 | 35 | 24 | Taqpath | UDI | 40 | 1 | 96.09±0.91 | 98.34 | 284.75Mbp | 0.27±0.35 | 11,390,135 | 443±9 | 38 | 0.270/0.020 | 192±31 |
| v19 | MiSeq | EUA (prelimary LoD and Positive and Negative patient samples) | 14 | 35 | 26 | Taqpath | UDI | 40 | 1 | 85.26±20.73 | 97.28 | 563.71Mbp | 0.50±0.49 | 22,548,216 | 1,052±47 | 38 | 0.011/0.000 | 189±27 |
| v18 | MiSeq | Negative Patient and attempted contrived EUA (high basecalling error rate, diagnostic for amplicon misassignment) | 11 | 30 | 27 | Taqpath | Semi-Combinatorial | 40 | 1 | 69.46±22.02 | 94.37 | 438.81Mbp | 1.25±0.62 | 17,552,240 | 1,042±57 | 38 | 0.008/0.000 | 192±22 |
| v17 | MiSeq | Negative Patient and attempted contrived EUA (but too high viral input for LoD experiment) | 17 | 30 | 26 | Taqpath | Semi-Combinatorial | 40 | 1 | 93.83±1.71 | 97.63 | 555.45Mbp | 0.13±0.01 | 22,218,176 | 934±12 | 38 | 0.006/0.036 | 175±21 |
| v16 | MiSeq | v13/v14 and Simulated Patients; first test no RPP30 unindexed | 17 | 30 | 31.3 | Taqpath | Combinatorial | 40 | 1 | 94.99±1.07 | 98.20 | 598.33Mbp | 0.22±0.34 | 23,933,240 | 973±24 | 38 | 0.032/0.000 | 193±31 |
| v15 | MiSeq | rerun V13 with 384-well plates 1-3; bleach wash | 18 | 30 | 40.8 | Taqpath | Combinatorial | 50 | 1 | 75.37±7.07 | 94.56 | 497.81Mbp | 0.83±0.51 | 19,912,204 | 1,103±45 | 38 | 0.027/0.078 | 177±20 |
| v14 | MiSeq | Saliva in NS diluted; Contrived in HEK extracted; no bleach wash | 17 | 30 | 40.8 | Taqpath | Combinatorial | 50 | 1 | 97.00±0.44 | 99.01 | 463.36Mbp | 0.12±0.01 | 18,534,400 | 742±13 | 38 | 0.138/0.101 | 203±24 |
| v13 | MiSeq | Saliva in NS diluted; Contrived in HEK extracted; Titrate Rxn Vols | 15 | 30 | 40.8 | Taqpath | Combinatorial | 50 | 1 | 97.16±0.97 | 98.96 | 274.97Mbp | 0.14±0.01 | 10,998,699 | 406±21 | 38 | 0.137/0.101 | 193±30 |
| v12 | MiSeq | MTS in TE diluted and titration of RPP30 unindexed primers | 44 | 40 | 20 | Taqpath | UDI | 50 | 1 | 93.18±0.96 | 97.35 | 171.26Mbp | 0.35±0.11 | 6,850,514 | 277±24 | 38 | 0.166/0.105 | 147±16 |
| v11 | MiSeq | MTS in TE diluted | 31 | 40 | 22 | Taqpath | UDI | 50 | 1 | 94.14±1.02 | 98.37 | 423.37Mbp | 0.52±0.13 | 16,934,964 | 703±31 | 38 | 0.090/0.064 | 152±21 |
| v10 | MiSeq | NP in NS real-world samples; Saliva in NS diluted | 36 | 40 | 20 | NEB Luna vs Taqpath | UDI | 50 | 1 | 94.33±0.93 | 97.94 | 440.62Mbp | 0.19±0.04 | 17,624,768 | 727±15 | 38 | 0.103/0.086 | 112±16 |
| v9 | MiSeq | MTS in NS diluted; NP in NS real-world samples | 28 | 40 | 20 | NEB Luna | UDI | 50 and 60 | 1 | 95.47±0.89 | 98.74 | 346.55Mbp | 0.48±0.08 | 13,862,051 | 563±20 | 38 | 0.095/0.029 | 172±26 |
| v8 | MiSeq | MTS in NS diluted | 39 | 40 | 20 | NEB Luna | UDI | 40 and 50 | 1 | 95.06±0.83 | 98.29 | 475.38Mbp | 0.16±0.02 | 19,015,232 | 776±11 | 38 | 0.084/0.043 | 146±18 |
| v7 | MiSeq | MTS in TE diluted; Saliva in TE with Protease +/- dilution | 37 | 40 | 16 | NEB Luna | UDI | 40 | 1 | 92.71±0.99 | 97.26 | 218.65Mbp | 0.67±0.32 | 8,745,975 | 363±31 | 38 | 0.102/0.044 | 190±34 |