Analyzing demux output from: merged Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv Loaded 776 rows from Demultiplex_Stats.csv ================================================================================ 1. % UNDETERMINED PER LANE ================================================================================ Undetermined Summary per Lane: %_Undetermined Undetermined_Reads Total_Reads Lane 1 7.73 309611837 4003982799 2 7.63 308632215 4042524069 3 7.72 310603780 4021848294 4 7.58 306145030 4038106205 5 7.42 302305448 4075270033 6 7.75 312709069 4033267142 7 7.55 309485428 4100159606 8 7.62 309533554 4060257736 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ No samples found with <1000000 reads ================================================================================ 3. NTC SAMPLES WITH >2000000 READS ================================================================================ No NTC samples found with >2000000 reads ================================================================================ 4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS) ================================================================================ Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv Lane 1 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3000 CCAGTCGTCA GGGGGGGGGG 8337867 0.2082 0.0258 3001 GCAATCTGCT TATTGCGCTA 6626387 0.1655 0.0205 3002 GAGCAGCTTG GGGGGGGGGG 6216276 0.1553 0.0192 3003 CCTAAGCTGA GGGGGGGGGG 5736898 0.1433 0.0177 3004 AGATTAGCGT GGGGGGGGGG 5584967 0.1395 0.0173 3005 AGTATCCGAT ACGAACCAAG 4857676 0.1213 0.0150 3006 TATCCGCGTC GGGGGGGGGG 4626144 0.1155 0.0143 3007 ATGACAGCAC GGGGGGGGGG 3892670 0.0972 0.0120 3008 TGGAGATCGA GGGGGGGGGG 3572485 0.0892 0.0110 3009 TAACTTGGTC GGGGGGGGGG 3513300 0.0877 0.0109 3010 GCCACCTAGT GGGGGGGGGG 2871254 0.0717 0.0089 3011 ACGAGACGTC GGGGGGGGGG 2825204 0.0706 0.0087 3012 TCCAACTGAA GGGGGGGGGG 2751699 0.0687 0.0085 3013 CGCACTGGTA GGGGGGGGGG 2128660 0.0532 0.0066 3014 CGATGTCTTG GGGGGGGGGG 2081455 0.0520 0.0064 Lane 2 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5000 CCAGTCGTCA GGGGGGGGGG 8218795 0.2033 0.0254 5001 GCAATCTGCT TATTGCGCTA 6685650 0.1654 0.0207 5002 GAGCAGCTTG GGGGGGGGGG 6219202 0.1538 0.0192 5003 CCTAAGCTGA GGGGGGGGGG 5685542 0.1406 0.0176 5004 AGATTAGCGT GGGGGGGGGG 5515228 0.1364 0.0170 5005 AGTATCCGAT ACGAACCAAG 4894697 0.1211 0.0151 5006 TATCCGCGTC GGGGGGGGGG 4584972 0.1134 0.0142 5007 ATGACAGCAC GGGGGGGGGG 3836934 0.0949 0.0119 5008 TGGAGATCGA GGGGGGGGGG 3524373 0.0872 0.0109 5009 TAACTTGGTC GGGGGGGGGG 3476291 0.0860 0.0107 5010 GCCACCTAGT GGGGGGGGGG 2825582 0.0699 0.0087 5011 ACGAGACGTC GGGGGGGGGG 2777107 0.0687 0.0086 5012 TCCAACTGAA GGGGGGGGGG 2720706 0.0673 0.0084 5013 CGCACTGGTA GGGGGGGGGG 2106267 0.0521 0.0065 Lane 3 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6000 CCAGTCGTCA GGGGGGGGGG 8197804 0.2038 0.0253 6001 GCAATCTGCT TATTGCGCTA 6667662 0.1658 0.0206 6002 GAGCAGCTTG GGGGGGGGGG 6111079 0.1519 0.0189 6003 CCTAAGCTGA GGGGGGGGGG 5706798 0.1419 0.0176 6004 AGATTAGCGT GGGGGGGGGG 5480667 0.1363 0.0169 6005 AGTATCCGAT ACGAACCAAG 4881117 0.1214 0.0151 6006 TATCCGCGTC GGGGGGGGGG 4538491 0.1128 0.0140 6007 ATGACAGCAC GGGGGGGGGG 3831730 0.0953 0.0118 6008 TAACTTGGTC GGGGGGGGGG 3470353 0.0863 0.0107 6009 TGGAGATCGA GGGGGGGGGG 3452974 0.0859 0.0107 6010 GCCACCTAGT GGGGGGGGGG 2778043 0.0691 0.0086 6011 ACGAGACGTC GGGGGGGGGG 2759015 0.0686 0.0085 6012 TCCAACTGAA GGGGGGGGGG 2666072 0.0663 0.0082 6013 CGCACTGGTA GGGGGGGGGG 2101461 0.0523 0.0065 6014 AACGAAGATC GGGGGGGGGG 2013499 0.0501 0.0062 Lane 4 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2000 CCAGTCGTCA GGGGGGGGGG 7981195 0.1976 0.0247 2001 GCAATCTGCT TATTGCGCTA 6706390 0.1661 0.0207 2002 GAGCAGCTTG GGGGGGGGGG 5969234 0.1478 0.0184 2003 CCTAAGCTGA GGGGGGGGGG 5551000 0.1375 0.0171 2004 AGATTAGCGT GGGGGGGGGG 5319979 0.1317 0.0164 2005 AGTATCCGAT ACGAACCAAG 4893989 0.1212 0.0151 2006 TATCCGCGTC GGGGGGGGGG 4440834 0.1100 0.0137 2007 ATGACAGCAC GGGGGGGGGG 3730100 0.0924 0.0115 2008 TAACTTGGTC GGGGGGGGGG 3412453 0.0845 0.0105 2009 TGGAGATCGA GGGGGGGGGG 3396409 0.0841 0.0105 2010 GCCACCTAGT GGGGGGGGGG 2762012 0.0684 0.0085 2011 ACGAGACGTC GGGGGGGGGG 2720072 0.0674 0.0084 2012 TCCAACTGAA GGGGGGGGGG 2631882 0.0652 0.0081 2013 CGCACTGGTA GGGGGGGGGG 2072402 0.0513 0.0064 Lane 5 - Found 13 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4000 CCAGTCGTCA GGGGGGGGGG 7779615 0.1909 0.0240 4001 GCAATCTGCT TATTGCGCTA 6742168 0.1654 0.0208 4002 GAGCAGCTTG GGGGGGGGGG 5978995 0.1467 0.0185 4003 CCTAAGCTGA GGGGGGGGGG 5440028 0.1335 0.0168 4004 AGATTAGCGT GGGGGGGGGG 5247951 0.1288 0.0162 4005 AGTATCCGAT ACGAACCAAG 4934511 0.1211 0.0152 4006 TATCCGCGTC GGGGGGGGGG 4379596 0.1075 0.0135 4007 ATGACAGCAC GGGGGGGGGG 3676119 0.0902 0.0114 4008 TGGAGATCGA GGGGGGGGGG 3336070 0.0819 0.0103 4009 TAACTTGGTC GGGGGGGGGG 3332825 0.0818 0.0103 4010 GCCACCTAGT GGGGGGGGGG 2728834 0.0670 0.0084 4011 ACGAGACGTC GGGGGGGGGG 2609258 0.0640 0.0081 4012 TCCAACTGAA GGGGGGGGGG 2571672 0.0631 0.0079 Lane 6 - Found 16 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7000 CCAGTCGTCA GGGGGGGGGG 8322877 0.2064 0.0257 7001 GCAATCTGCT TATTGCGCTA 6659067 0.1651 0.0206 7002 GAGCAGCTTG GGGGGGGGGG 6266557 0.1554 0.0194 7003 CCTAAGCTGA GGGGGGGGGG 5774365 0.1432 0.0178 7004 AGATTAGCGT GGGGGGGGGG 5556283 0.1378 0.0172 7005 AGTATCCGAT ACGAACCAAG 4893501 0.1213 0.0151 7006 TATCCGCGTC GGGGGGGGGG 4643234 0.1151 0.0143 7007 ATGACAGCAC GGGGGGGGGG 3892918 0.0965 0.0120 7008 TGGAGATCGA GGGGGGGGGG 3582790 0.0888 0.0111 7009 TAACTTGGTC GGGGGGGGGG 3531914 0.0876 0.0109 7010 GCCACCTAGT GGGGGGGGGG 2900210 0.0719 0.0090 7011 ACGAGACGTC GGGGGGGGGG 2845011 0.0705 0.0088 7012 TCCAACTGAA GGGGGGGGGG 2752254 0.0682 0.0085 7013 CGCACTGGTA GGGGGGGGGG 2164687 0.0537 0.0067 7014 AACGAAGATC GGGGGGGGGG 2057071 0.0510 0.0064 7015 CGATGTCTTG GGGGGGGGGG 2048933 0.0508 0.0063 Lane 7 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1000 CCAGTCGTCA GGGGGGGGGG 8219668 0.2005 0.0254 1001 GCAATCTGCT TATTGCGCTA 6764398 0.1650 0.0209 1002 GAGCAGCTTG GGGGGGGGGG 6412469 0.1564 0.0198 1003 CCTAAGCTGA GGGGGGGGGG 5712062 0.1393 0.0176 1004 AGATTAGCGT GGGGGGGGGG 5576424 0.1360 0.0172 1005 AGTATCCGAT ACGAACCAAG 4973970 0.1213 0.0154 1006 TATCCGCGTC GGGGGGGGGG 4651953 0.1135 0.0144 1007 ATGACAGCAC GGGGGGGGGG 3874521 0.0945 0.0120 1008 TGGAGATCGA GGGGGGGGGG 3567567 0.0870 0.0110 1009 TAACTTGGTC GGGGGGGGGG 3490969 0.0851 0.0108 1010 GCCACCTAGT GGGGGGGGGG 2897296 0.0707 0.0089 1011 ACGAGACGTC GGGGGGGGGG 2750559 0.0671 0.0085 1012 TCCAACTGAA GGGGGGGGGG 2741406 0.0669 0.0085 1013 CGCACTGGTA GGGGGGGGGG 2076488 0.0506 0.0064 1014 AACGAAGATC GGGGGGGGGG 2068909 0.0505 0.0064 Lane 8 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 CCAGTCGTCA GGGGGGGGGG 8497299 0.2093 0.0262 1 GCAATCTGCT TATTGCGCTA 6663183 0.1641 0.0206 2 GAGCAGCTTG GGGGGGGGGG 6512598 0.1604 0.0201 3 CCTAAGCTGA GGGGGGGGGG 5756659 0.1418 0.0178 4 AGATTAGCGT GGGGGGGGGG 5723431 0.1410 0.0177 5 AGTATCCGAT ACGAACCAAG 4918985 0.1211 0.0152 6 TATCCGCGTC GGGGGGGGGG 4749606 0.1170 0.0147 7 ATGACAGCAC GGGGGGGGGG 3950628 0.0973 0.0122 8 TGGAGATCGA GGGGGGGGGG 3656756 0.0901 0.0113 9 TAACTTGGTC GGGGGGGGGG 3521939 0.0867 0.0109 10 GCCACCTAGT GGGGGGGGGG 2896098 0.0713 0.0089 11 ACGAGACGTC GGGGGGGGGG 2825337 0.0696 0.0087 12 TCCAACTGAA GGGGGGGGGG 2825222 0.0696 0.0087 13 CGCACTGGTA GGGGGGGGGG 2093256 0.0516 0.0065 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ No barcodes found with >20.0% mismatch rate ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 7.63% Status: 🟡 WARNING Reason(s): Overall undetermined 7.63% >= 5.0% Thresholds: <5.0% = PASS, 5.0-10.0% = WARNING, >10.0% = FAIL NTC gate: >2,000,000 reads = FAIL === Creating reports in . === QC summary saved to: ./qc_report.csv Detailed QC report saved to: ./qc_report_detailed.txt Warning file created: ./samplesheet_status.warning ================================================================================ QC SUMMARY ================================================================================ Metric Value Total_Reads 32375415884 Total_Samples_Analyzed 97 Number_of_Lanes 8 Global_Percent_Undetermined 7.63% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 0 NTC_Samples_with_High_Reads 0 Significant_Unknown_Barcodes 116 High_Mismatch_Barcodes 0 Final_Status WARNING ================================================================================ QC Analysis completed successfully! Flowcell Status: WARNING Reports generated: - ./qc_report.csv - ./qc_report_detailed.txt - ./samplesheet_status.warning ================================================================================