|
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
|
- aObtained from output of Porechop
- bObtained from output of LAclust
- cObtained from output of BWA-MEM. Input into BWA-MEM was limited to 200 reads based on LAclust options
- dConsensus sequence identity to the reference sequence of NDV LaSota sequenced with MiSeq
- (MH392212/chicken/USA/LaSota/1946)
- eEach dilution performed in duplicate and threshold cycle (Ct) values from each well are shown here
- fRun 1
- gRun 2
- 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
