Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 776 rows from Demultiplex_Stats.csv
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1. % UNDETERMINED PER LANE
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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
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2. SAMPLES WITH <1000000 READS (NON-NTC)
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No samples found with <1000000 reads
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3. NTC SAMPLES WITH >2000000 READS
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No NTC samples found with >2000000 reads
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4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS)
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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
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5. BARCODES WITH HIGH MISMATCH RATES
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No barcodes found with >20.0% mismatch rate
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FINAL STATUS CHECK
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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
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QC SUMMARY
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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
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QC Analysis completed successfully!
Flowcell Status: WARNING
Reports generated:
- ./qc_report.csv
- ./qc_report_detailed.txt
- ./samplesheet_status.warning
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