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Table 1 Comparison of MinION sequencing to RT-qPCR for detection of NDV LaSota (runs 1 and 2)

From: Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

Dilution (EID50/ml) Total readsa Total NDV readsb Reads per consensusc Percent identityd Consensus length RT-qPCRe (Ct)
R1f | R2g R1 | R2 R1 | R2 R1 | R2 R1 | R2 R1 | R2
10^6 6667 | 11,366 6577 | 10,861 200 | 200 100 | 100 734 | 734 21.8, 21.1 | 22.7, 22.7
10^5 4519 | 6801 4439 | 6540 200 | 200 100 | 100 734 | 734 26.3, 25.8 | 26.2, 26.4
10^4 3856 | 8289 3829 | 7890 200 | 200 100 | 100 734 | 734 28.9, 27.8 | 29.1, 29.3
10^3 164 | 9484 157 | 9061 157 | 200 100 | 100 734 | 734 31.4, 31.1 | 32.7, 32.8
10^2 94 | 4939 85 | 4725 85 | 200 100 | 100 734 | 734 34.2, 34.8 | 34.8, 35.3
10^1 133 | 2652 131 | 2520 131 | 200 99.04 | 99.86 729 | 734 34.9, 34.8 | 36.9, 36.7
  1. aObtained from output of Porechop
  2. bObtained from output of LAclust
  3. cObtained from output of BWA-MEM. Input into BWA-MEM was limited to 200 reads based on LAclust options
  4. dConsensus sequence identity to the reference sequence of NDV LaSota sequenced with MiSeq
  5. (MH392212/chicken/USA/LaSota/1946)
  6. eEach dilution performed in duplicate and threshold cycle (Ct) values from each well are shown here
  7. fRun 1
  8. gRun 2
  9. Note: All 60,000 reads obtained during 32 min of sequencing run (R1) were utilized for the analysis. All 98,916 reads from R2 were utilized for the analysis