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Table 2 Level of contamination for PCR-free library on BGISEQ-500

From: Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform

a. Sample arrangement of PCR-free library (HPV)
 Template YH-1 HPV11 + YH YH-1 YH-1 YH-1 YH-1 H2O-1 YH-1 YH-1 YH-1 YH-1 YH-1 Barcode 1
 Sample index MGIP-1 MGIP-2 MGIP-3 MGIP-4 MGIP-5 MGIP-6 MGIP-7 MGIP-8 MGIP-9 MGIP-10 MGIP-11 MGIP-12
 Template YH-2 YH-2 H2O-2 YH-2 YH-2 YH-2 YH-2 YH-2 YH-2 HPV18 + YH YH-2 YH-2 Barcode 2
 Sample index MGIP-13 MGIP-14 MGIP-15 MGIP-16 MGIP-17 MGIP-18 MGIP-19 MGIP-20 MGIP-21 MGIP-22 MGIP-23 MGIP-24
 Template YH-3 YH-3 YH-3 YH-3 HPV31 + YH YH-3 YH-3 YH-3 YH-3 YH-3 YH-3 YH-3 Barcode 3
 Sample index MGIP-25 MGIP-26 MGIP-27 MGIP-97 MGIP-29 MGIP-30 MGIP-31 MGIP-32 MGIP-33 MGIP-34 MGIP-35 MGIP-36
 Template YH-4 YH-4 YH-4 YH-4 YH-4 YH-4 HPV33 + YH YH-4 YH-4 YH-4 YH-4 YH-4 Barcode 4
 Sample index MGIP-37 MGIP-38 MGIP-39 MGIP-40 MGIP-41 MGIP-42 MGIP-43 MGIP-44 MGIP-45 MGIP-46 MGIP-47 MGIP-48
 Template HPV52 + YH YH-5 YH-5 YH-5 YH-5 H2O-5 YH-5 YH-5 YH-5 YH-5 YH-5 YH-5 Barcode 5
 Sample index MGIP-49 MGIP-50 MGIP-51 MGIP-52 MGIP-53 MGIP-54 MGIP-55 MGIP-56 MGIP-57 MGIP-58 MGIP-59 MGIP-60
 Template YH-6 YH-6 YH-6 YH-6 YH-6 YH-6 YH-6 H2O-6 HPV45 + 11 + YH YH-6 YH-6 YH-6 Barcode 6
 Sample index MGIP-61 MGIP-62 MGIP-63 MGIP-64 MGIP-65 MGIP-66 MGIP-67 MGIP-68 MGIP-69 MGIP-70 MGIP-71 MGIP-72
b. Performance of SeqHPV
 Library  Index Sample Index Total Reads Mapped Reads Mapped Rate Major Types HBB Score (0-10) HPV Score (0-10) False Positive False Negative     
 1 MGIP002 2470768 1800287 72.90% HPV11,HBB 10 10 0 0     
 2 MGIP022 2653747 2526477 95.20% HPV18,HBB 10 10 0 0     
 3 MGIP029 1793620 690665 94.30% HPV31,HBB 10 10 0 0     
 4 MGIP043 1511740 1210189 80.10% HPV33,HBB 10 10 0 0     
 5 MGIP049 1641545 1447782 88.20% HPV52,HBB 10 10 0 0     
 6 MGIP069 2800830 1942883 69.40% HPV45,HPV11,HBB 10 10 0 0     
 8 MGIP002 8 4 50.00% HPV11,HBB 5 10 0 0     
MGIP029 4 3 75.00% HPV31 0 10       
MGIP049 17 16 94.10% HPV52 0 10       
MGIP069 11 7 63.60% HPV45,HBB 10 10       
c. Index contamination rate of PCR-free libraries
  Library index HBB HPV11 HPV18 HPV31 HPV33 HPV52 HPV45      
 Read depth 1 2994608 1348826 83 36 14 23 33      
2 2722311 75 2310955 31 17 24 31      
3 1891540 53 65 1566954 10 8 15      
4 2936888 54 90 80 940365 18 25      
5 2289158 61 52 14 14 1237126 22      
6 1747934 253390 53 17 9 18 1497716      
8 27 3 0 3 0 16 5      
 Percent of read depth 1   14.7309% 0.0009% 0.0004% 0.0002% 0.0003% 0.0004%      
2   0.0008% 25.2386% 0.0003% 0.0002% 0.0003% 0.0003%      
3   0.0006% 0.0007% 17.1132% 0.0001% 0.0001% 0.0002%      
4   0.0006% 0.0010% 0.0009% 10.2700% 0.0002% 0.0003%      
5   0.0007% 0.0006% 0.0003% 0.0002% 13.5110% 0.0002%      
6   2.7673% 0.0006% 0.0002% 0.0001% 0.0002% 16.3570%      
8   0.0000% 0.0000% 0.0000% 0.0000% 0.0002% 0.0001%      
  1. a. Positive samples are in italic bold, negative samples with YH genome only are in black font, water controls are bolded and sample index are in italic. b. Empty controls are in italic. Index 7 data was excluded due to its oligo synthesis contamination. c. Italic bold, proper combinations; italic, improper combinations. The average sample-to-sample mis-assignment rate is 0.0004% without any filtering