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 7.42 293146516 3949083474 2 7.56 298323753 3944247355 3 7.52 300084169 3991640170 4 8.11 320493726 3953564323 5 7.80 306473228 3928620214 6 7.38 291458533 3951964639 7 7.40 293572378 3969347905 8 7.47 295033479 3951217964 ================================================================================ 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 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4000 GAGCAGCTTG GGGGGGGGGG 6537395 0.1655 0.0207 4001 AGATTAGCGT GGGGGGGGGG 5535460 0.1402 0.0175 4002 TATCCGCGTC GGGGGGGGGG 4892126 0.1239 0.0155 4003 ATGACAGCAC GGGGGGGGGG 4182645 0.1059 0.0132 4004 CCTAAGCTGA GGGGGGGGGG 4111586 0.1041 0.0130 4005 TGGAGATCGA GGGGGGGGGG 3446135 0.0873 0.0109 4006 ACGAGACGTC GGGGGGGGGG 3156661 0.0799 0.0100 4007 CCAGTCGTCA GGGGGGGGGG 2937326 0.0744 0.0093 4008 TCCAACTGAA GGGGGGGGGG 2769644 0.0701 0.0088 4009 TAACTTGGTC GGGGGGGGGG 2761038 0.0699 0.0087 4010 CAACTGCGCA GGGGGGGGGG 2748459 0.0696 0.0087 4011 GCCACCTAGT GGGGGGGGGG 2495508 0.0632 0.0079 4012 CCGATAGTAG GGGGGGGGGG 2366714 0.0599 0.0075 4013 AGAAGACCTA GGGGGGGGGG 2119381 0.0537 0.0067 Lane 2 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3000 GAGCAGCTTG GGGGGGGGGG 6641120 0.1684 0.0210 3001 AGATTAGCGT GGGGGGGGGG 5449301 0.1382 0.0172 3002 TATCCGCGTC GGGGGGGGGG 4955465 0.1256 0.0157 3003 ATGACAGCAC GGGGGGGGGG 4211400 0.1068 0.0133 3004 CCTAAGCTGA GGGGGGGGGG 4087443 0.1036 0.0129 3005 TGGAGATCGA GGGGGGGGGG 3537594 0.0897 0.0112 3006 ACGAGACGTC GGGGGGGGGG 3187855 0.0808 0.0101 3007 CCAGTCGTCA GGGGGGGGGG 2890989 0.0733 0.0091 3008 CAACTGCGCA GGGGGGGGGG 2856930 0.0724 0.0090 3009 TCCAACTGAA GGGGGGGGGG 2799089 0.0710 0.0088 3010 TAACTTGGTC GGGGGGGGGG 2785889 0.0706 0.0088 3011 GCCACCTAGT GGGGGGGGGG 2638597 0.0669 0.0083 3012 CCGATAGTAG GGGGGGGGGG 2461817 0.0624 0.0078 3013 AGAAGACCTA GGGGGGGGGG 2230135 0.0565 0.0070 Lane 3 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1000 GAGCAGCTTG GGGGGGGGGG 6378005 0.1598 0.0202 1001 AGATTAGCGT GGGGGGGGGG 5382754 0.1349 0.0170 1002 TATCCGCGTC GGGGGGGGGG 4776580 0.1197 0.0151 1003 ATGACAGCAC GGGGGGGGGG 4057071 0.1016 0.0128 1004 CCTAAGCTGA GGGGGGGGGG 3980784 0.0997 0.0126 1005 TGGAGATCGA GGGGGGGGGG 3375513 0.0846 0.0107 1006 ACGAGACGTC GGGGGGGGGG 3141988 0.0787 0.0099 1007 CCAGTCGTCA GGGGGGGGGG 2833223 0.0710 0.0090 1008 CAACTGCGCA GGGGGGGGGG 2722088 0.0682 0.0086 1009 TCCAACTGAA GGGGGGGGGG 2686627 0.0673 0.0085 1010 TAACTTGGTC GGGGGGGGGG 2665861 0.0668 0.0084 1011 GCCACCTAGT GGGGGGGGGG 2574254 0.0645 0.0081 1012 CCGATAGTAG GGGGGGGGGG 2499674 0.0626 0.0079 1013 AGAAGACCTA GGGGGGGGGG 2211202 0.0554 0.0070 Lane 4 - Found 17 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6000 GAGCAGCTTG GGGGGGGGGG 6227501 0.1575 0.0197 6001 AGATTAGCGT GGGGGGGGGG 5292554 0.1339 0.0167 6002 TATCCGCGTC GGGGGGGGGG 4778675 0.1209 0.0151 6003 ATGACAGCAC GGGGGGGGGG 4008656 0.1014 0.0127 6004 CCTAAGCTGA GGGGGGGGGG 3808092 0.0963 0.0120 6005 TGGAGATCGA GGGGGGGGGG 3434181 0.0869 0.0109 6006 ACGAGACGTC GGGGGGGGGG 3124039 0.0790 0.0099 6007 CCAGTCGTCA GGGGGGGGGG 2820524 0.0713 0.0089 6008 CAACTGCGCA GGGGGGGGGG 2796171 0.0707 0.0088 6009 GCCACCTAGT GGGGGGGGGG 2783808 0.0704 0.0088 6010 TCCAACTGAA GGGGGGGGGG 2718936 0.0688 0.0086 6011 TAACTTGGTC GGGGGGGGGG 2611712 0.0661 0.0083 6012 CCGATAGTAG GGGGGGGGGG 2570494 0.0650 0.0081 6013 AGAAGACCTA GGGGGGGGGG 2517039 0.0637 0.0080 6014 CGATGTCTTG GGGGGGGGGG 2218670 0.0561 0.0070 6015 ATGTTGCCAC GGGGGGGGGG 2152189 0.0544 0.0068 6016 TCGACGGCAA GGGGGGGGGG 2085748 0.0528 0.0066 Lane 5 - Found 17 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2000 GAGCAGCTTG GGGGGGGGGG 6242873 0.1589 0.0197 2001 AGATTAGCGT GGGGGGGGGG 5214857 0.1327 0.0165 2002 TATCCGCGTC GGGGGGGGGG 4728492 0.1204 0.0149 2003 ATGACAGCAC GGGGGGGGGG 3979820 0.1013 0.0126 2004 CCTAAGCTGA GGGGGGGGGG 3839783 0.0977 0.0121 2005 TGGAGATCGA GGGGGGGGGG 3376821 0.0860 0.0107 2006 ACGAGACGTC GGGGGGGGGG 3082398 0.0785 0.0097 2007 CCAGTCGTCA GGGGGGGGGG 2780589 0.0708 0.0088 2008 CAACTGCGCA GGGGGGGGGG 2741802 0.0698 0.0087 2009 GCCACCTAGT GGGGGGGGGG 2689826 0.0685 0.0085 2010 TCCAACTGAA GGGGGGGGGG 2683410 0.0683 0.0085 2011 TAACTTGGTC GGGGGGGGGG 2610255 0.0664 0.0082 2012 CCGATAGTAG GGGGGGGGGG 2474120 0.0630 0.0078 2013 AGAAGACCTA GGGGGGGGGG 2383841 0.0607 0.0075 2014 ATGTTGCCAC GGGGGGGGGG 2055462 0.0523 0.0065 2015 CGATGTCTTG GGGGGGGGGG 2011793 0.0512 0.0064 2016 TCGACGGCAA GGGGGGGGGG 1964893 0.0500 0.0062 Lane 6 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 GAGCAGCTTG GGGGGGGGGG 6449352 0.1632 0.0204 1 AGATTAGCGT GGGGGGGGGG 5364438 0.1357 0.0170 2 TATCCGCGTC GGGGGGGGGG 4815778 0.1219 0.0152 3 ATGACAGCAC GGGGGGGGGG 4094210 0.1036 0.0129 4 CCTAAGCTGA GGGGGGGGGG 4022061 0.1018 0.0127 5 TGGAGATCGA GGGGGGGGGG 3361130 0.0850 0.0106 6 ACGAGACGTC GGGGGGGGGG 3133017 0.0793 0.0099 7 CCAGTCGTCA GGGGGGGGGG 2865502 0.0725 0.0091 8 TAACTTGGTC GGGGGGGGGG 2705186 0.0685 0.0085 9 CAACTGCGCA GGGGGGGGGG 2698089 0.0683 0.0085 10 TCCAACTGAA GGGGGGGGGG 2697029 0.0682 0.0085 11 GCCACCTAGT GGGGGGGGGG 2487933 0.0630 0.0079 12 CCGATAGTAG GGGGGGGGGG 2392073 0.0605 0.0076 13 AGAAGACCTA GGGGGGGGGG 2097662 0.0531 0.0066 Lane 7 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5000 GAGCAGCTTG GGGGGGGGGG 6702560 0.1689 0.0212 5001 AGATTAGCGT GGGGGGGGGG 5508059 0.1388 0.0174 5002 TATCCGCGTC GGGGGGGGGG 5015938 0.1264 0.0159 5003 ATGACAGCAC GGGGGGGGGG 4212559 0.1061 0.0133 5004 CCTAAGCTGA GGGGGGGGGG 4158571 0.1048 0.0131 5005 TGGAGATCGA GGGGGGGGGG 3497305 0.0881 0.0111 5006 ACGAGACGTC GGGGGGGGGG 3259877 0.0821 0.0103 5007 CCAGTCGTCA GGGGGGGGGG 2958389 0.0745 0.0094 5008 TAACTTGGTC GGGGGGGGGG 2807282 0.0707 0.0089 5009 TCCAACTGAA GGGGGGGGGG 2789612 0.0703 0.0088 5010 CAACTGCGCA GGGGGGGGGG 2788825 0.0703 0.0088 5011 GCCACCTAGT GGGGGGGGGG 2528852 0.0637 0.0080 5012 CCGATAGTAG GGGGGGGGGG 2436517 0.0614 0.0077 5013 AGAAGACCTA GGGGGGGGGG 2130169 0.0537 0.0067 Lane 8 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7000 GAGCAGCTTG GGGGGGGGGG 6702867 0.1696 0.0212 7001 AGATTAGCGT GGGGGGGGGG 5609892 0.1420 0.0177 7002 TATCCGCGTC GGGGGGGGGG 5015601 0.1269 0.0159 7003 ATGACAGCAC GGGGGGGGGG 4275974 0.1082 0.0135 7004 CCTAAGCTGA GGGGGGGGGG 4227752 0.1070 0.0134 7005 TGGAGATCGA GGGGGGGGGG 3480219 0.0881 0.0110 7006 ACGAGACGTC GGGGGGGGGG 3239709 0.0820 0.0102 7007 CCAGTCGTCA GGGGGGGGGG 3009166 0.0762 0.0095 7008 TAACTTGGTC GGGGGGGGGG 2839678 0.0719 0.0090 7009 TCCAACTGAA GGGGGGGGGG 2788726 0.0706 0.0088 7010 CAACTGCGCA GGGGGGGGGG 2732388 0.0692 0.0086 7011 GCCACCTAGT GGGGGGGGGG 2492932 0.0631 0.0079 7012 CCGATAGTAG GGGGGGGGGG 2395457 0.0606 0.0076 7013 AGAAGACCTA GGGGGGGGGG 2078966 0.0526 0.0066 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ No barcodes found with >20.0% mismatch rate ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 7.58% Status: 🟡 WARNING Reason(s): Overall undetermined 7.58% >= 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 31639686044 Total_Samples_Analyzed 97 Number_of_Lanes 8 Global_Percent_Undetermined 7.58% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 0 NTC_Samples_with_High_Reads 0 Significant_Unknown_Barcodes 118 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 ================================================================================