Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 392 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 5.52 221059769 4004297187
2 5.90 225513465 3822265332
3 5.35 200487374 3746919997
4 5.32 200329565 3768247701
5 4.74 171826374 3628757465
6 4.75 184145712 3874163237
7 4.94 190151678 3850667784
8 5.09 202217613 3974555505
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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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Found 1 NTC samples with >2000000 reads:
SampleID Index # Reads
0 NTC_0001_0001_23KMKGLT4_1 GATCTGTATG-ATCGAAGAGC 3096639
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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 23 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4001 CTCACCAGTT GGGGGGGGGG 8458630 0.2112 0.0276
4002 TAGAAGATCG GGGGGGGGGG 7394299 0.1847 0.0241
4003 AGTCCAGCGT GGGGGGGGGG 7306092 0.1825 0.0238
4004 AATAGACTGC GGGGGGGGGG 5668678 0.1416 0.0185
4005 AGGACGGACA GGGGGGGGGG 4620766 0.1154 0.0151
4006 GCGAAGTAGG CAGGCCATGT 4572171 0.1142 0.0149
4007 CATCACCTAA GGGGGGGGGG 4463209 0.1115 0.0146
4008 ACGGTCGCAT CGTCATCGAA 4368466 0.1091 0.0142
4009 CCTGGAATTA GGGGGGGGGG 3811715 0.0952 0.0124
4010 CGGCATATAC GGGGGGGGGG 3713173 0.0927 0.0121
4011 GCGACTCGTA ACCATTGTGT 3307477 0.0826 0.0108
4012 GCGACTCGTA GGGGGGGGGG 3287995 0.0821 0.0107
4013 CAACGTTGAC GGGGGGGGGG 3189964 0.0797 0.0104
4014 ATGATCAACG GGGGGGGGGG 3151810 0.0787 0.0103
4015 AGGCAGCCAT GGGGGGGGGG 3149692 0.0787 0.0103
4016 TGTTACAGAG CGTCATCGAA 2979753 0.0744 0.0097
4017 ACGGTCGCAT AAGCTATAGC 2870719 0.0717 0.0094
4018 GCGCGGTTAA GGGGGGGGGG 2790916 0.0697 0.0091
4019 TTCAGATCCA GGGGGGGGGG 2789274 0.0697 0.0091
4020 GCGCGGTTAA GTACTCTCTA 2722580 0.0680 0.0089
4021 CCTATGTGTA GGGGGGGGGG 2607642 0.0651 0.0085
4022 CCTGGAATTA TGTGTACCAG 2290216 0.0572 0.0075
4023 CCTGGAATTA GTACTCTCTA 2016250 0.0504 0.0066
Lane 2 - Found 22 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5001 CTCACCAGTT GGGGGGGGGG 6725259 0.1759 0.0219
5002 AGTCCAGCGT GGGGGGGGGG 5750923 0.1505 0.0188
5003 TAGAAGATCG GGGGGGGGGG 5489139 0.1436 0.0179
5004 AATAGACTGC GGGGGGGGGG 4332307 0.1133 0.0141
5005 GCGAAGTAGG CAGGCCATGT 4076991 0.1067 0.0133
5006 ACGGTCGCAT CGTCATCGAA 3904348 0.1021 0.0127
5007 CATCACCTAA GGGGGGGGGG 3517635 0.0920 0.0115
5008 AGGACGGACA GGGGGGGGGG 3494155 0.0914 0.0114
5009 CCTGGAATTA GGGGGGGGGG 3012663 0.0788 0.0098
5010 CGGCATATAC GGGGGGGGGG 2945794 0.0771 0.0096
5011 GCGACTCGTA ACCATTGTGT 2944708 0.0770 0.0096
5012 TGTTACAGAG CGTCATCGAA 2654226 0.0694 0.0087
5013 ACGGTCGCAT AAGCTATAGC 2577659 0.0674 0.0084
5014 CAACGTTGAC GGGGGGGGGG 2488362 0.0651 0.0081
5015 AGGCAGCCAT GGGGGGGGGG 2463579 0.0645 0.0080
5016 GCGACTCGTA GGGGGGGGGG 2438677 0.0638 0.0080
5017 GCGCGGTTAA GTACTCTCTA 2432896 0.0637 0.0079
5018 ATGATCAACG GGGGGGGGGG 2432085 0.0636 0.0079
5019 TTCAGATCCA GGGGGGGGGG 2168461 0.0567 0.0071
5020 GCGCGGTTAA GGGGGGGGGG 2101575 0.0550 0.0069
5021 CCTATGTGTA GGGGGGGGGG 2076137 0.0543 0.0068
5022 CCTGGAATTA TGTGTACCAG 2056470 0.0538 0.0067
Lane 3 - Found 22 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1001 CTCACCAGTT GGGGGGGGGG 6353099 0.1696 0.0207
1002 AGTCCAGCGT GGGGGGGGGG 5195636 0.1387 0.0169
1003 TAGAAGATCG GGGGGGGGGG 4880808 0.1303 0.0159
1004 GCGAAGTAGG CAGGCCATGT 4151455 0.1108 0.0135
1005 AATAGACTGC GGGGGGGGGG 4031237 0.1076 0.0131
1006 ACGGTCGCAT CGTCATCGAA 3987944 0.1064 0.0130
1007 CATCACCTAA GGGGGGGGGG 3349193 0.0894 0.0109
1008 AGGACGGACA GGGGGGGGGG 3196524 0.0853 0.0104
1009 GCGACTCGTA ACCATTGTGT 3006908 0.0803 0.0098
1010 CGGCATATAC GGGGGGGGGG 2881372 0.0769 0.0094
1011 CCTGGAATTA GGGGGGGGGG 2827073 0.0755 0.0092
1012 TGTTACAGAG CGTCATCGAA 2704405 0.0722 0.0088
1013 ACGGTCGCAT AAGCTATAGC 2627111 0.0701 0.0086
1014 GCGCGGTTAA GTACTCTCTA 2496230 0.0666 0.0081
1015 AGGCAGCCAT GGGGGGGGGG 2457459 0.0656 0.0080
1016 CAACGTTGAC GGGGGGGGGG 2412657 0.0644 0.0079
1017 ATGATCAACG GGGGGGGGGG 2345782 0.0626 0.0076
1018 GCGACTCGTA GGGGGGGGGG 2318844 0.0619 0.0076
1019 CCTATGTGTA GGGGGGGGGG 2111070 0.0563 0.0069
1020 TTCAGATCCA GGGGGGGGGG 2107300 0.0562 0.0069
1021 CCTGGAATTA TGTGTACCAG 2081886 0.0556 0.0068
1022 GCGCGGTTAA GGGGGGGGGG 2033531 0.0543 0.0066
Lane 4 - Found 23 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6001 CTCACCAGTT GGGGGGGGGG 6049099 0.1605 0.0197
6002 AGTCCAGCGT GGGGGGGGGG 4946219 0.1313 0.0161
6003 TAGAAGATCG GGGGGGGGGG 4612384 0.1224 0.0150
6004 GCGAAGTAGG CAGGCCATGT 4281644 0.1136 0.0140
6005 ACGGTCGCAT CGTCATCGAA 4068746 0.1080 0.0133
6006 AATAGACTGC GGGGGGGGGG 3800972 0.1009 0.0124
6007 CATCACCTAA GGGGGGGGGG 3251052 0.0863 0.0106
6008 GCGACTCGTA ACCATTGTGT 3071285 0.0815 0.0100
6009 AGGACGGACA GGGGGGGGGG 3021813 0.0802 0.0099
6010 CGGCATATAC GGGGGGGGGG 2816660 0.0747 0.0092
6011 TGTTACAGAG CGTCATCGAA 2757669 0.0732 0.0090
6012 CCTGGAATTA GGGGGGGGGG 2725624 0.0723 0.0089
6013 ACGGTCGCAT AAGCTATAGC 2687520 0.0713 0.0088
6014 GCGCGGTTAA GTACTCTCTA 2562849 0.0680 0.0084
6015 AGGCAGCCAT GGGGGGGGGG 2398519 0.0637 0.0078
6016 CAACGTTGAC GGGGGGGGGG 2344071 0.0622 0.0076
6017 ATGATCAACG GGGGGGGGGG 2256026 0.0599 0.0074
6018 GCGACTCGTA GGGGGGGGGG 2234566 0.0593 0.0073
6019 CCTGGAATTA TGTGTACCAG 2126765 0.0564 0.0069
6020 CCTATGTGTA GGGGGGGGGG 2114862 0.0561 0.0069
6021 TTCAGATCCA GGGGGGGGGG 2042821 0.0542 0.0067
6022 GCGCGGTTAA GGGGGGGGGG 1980505 0.0526 0.0065
6023 CCTGGAATTA GTACTCTCTA 1892375 0.0502 0.0062
Lane 5 - Found 9 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 CCAGTGCACT GGGGGGGGGG 8539896 0.2353 0.0278
1 TTGGATTGTC GGGGGGGGGG 4910547 0.1353 0.0160
2 CATCAGGCGT GGGGGGGGGG 4439230 0.1223 0.0145
3 ACAATAGCAC GGGGGGGGGG 3094884 0.0853 0.0101
4 AATTGGCACA GGGGGGGGGG 2733163 0.0753 0.0089
5 GTACGCATCG GGGGGGGGGG 2701236 0.0744 0.0088
6 TGCAACACTA GGGGGGGGGG 2660121 0.0733 0.0087
7 GAAGCAAGCG GGGGGGGGGG 1876059 0.0517 0.0061
8 CCACCTGCTT GGGGGGGGGG 1827986 0.0504 0.0060
Lane 6 - Found 10 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2001 CCAGTGCACT GGGGGGGGGG 11955380 0.3086 0.0390
2002 TTGGATTGTC GGGGGGGGGG 6822504 0.1761 0.0222
2003 CATCAGGCGT GGGGGGGGGG 6072888 0.1568 0.0198
2004 ACAATAGCAC GGGGGGGGGG 4081883 0.1054 0.0133
2005 AATTGGCACA GGGGGGGGGG 3718466 0.0960 0.0121
2006 GTACGCATCG GGGGGGGGGG 3573840 0.0922 0.0117
2007 TGCAACACTA GGGGGGGGGG 3383154 0.0873 0.0110
2008 GAAGCAAGCG GGGGGGGGGG 2685584 0.0693 0.0088
2009 CCACCTGCTT GGGGGGGGGG 2217437 0.0572 0.0072
2010 TCGCATGACA GGGGGGGGGG 2075737 0.0536 0.0068
Lane 7 - Found 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3001 CCAGTGCACT GGGGGGGGGG 12520817 0.3252 0.0408
3002 TTGGATTGTC GGGGGGGGGG 7190619 0.1867 0.0234
3003 CATCAGGCGT GGGGGGGGGG 6398853 0.1662 0.0209
3004 ACAATAGCAC GGGGGGGGGG 4262477 0.1107 0.0139
3005 AATTGGCACA GGGGGGGGGG 3935036 0.1022 0.0128
3006 GTACGCATCG GGGGGGGGGG 3781413 0.0982 0.0123
3007 TGCAACACTA GGGGGGGGGG 3522018 0.0915 0.0115
3008 GAAGCAAGCG GGGGGGGGGG 2870324 0.0745 0.0094
3009 CCACCTGCTT GGGGGGGGGG 2310566 0.0600 0.0075
3010 TCGCATGACA GGGGGGGGGG 2172931 0.0564 0.0071
3011 AGTACAACTG GGGGGGGGGG 1973818 0.0513 0.0064
Lane 8 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7001 CCAGTGCACT GGGGGGGGGG 13808902 0.3474 0.0450
7002 TTGGATTGTC GGGGGGGGGG 8055516 0.2027 0.0263
7003 CATCAGGCGT GGGGGGGGGG 7292412 0.1835 0.0238
7004 ACAATAGCAC GGGGGGGGGG 4755613 0.1197 0.0155
7005 AATTGGCACA GGGGGGGGGG 4462422 0.1123 0.0145
7006 GTACGCATCG GGGGGGGGGG 4370742 0.1100 0.0143
7007 TGCAACACTA GGGGGGGGGG 3938302 0.0991 0.0128
7008 GAAGCAAGCG GGGGGGGGGG 3465446 0.0872 0.0113
7009 CCACCTGCTT GGGGGGGGGG 2611613 0.0657 0.0085
7010 TCGCATGACA GGGGGGGGGG 2436248 0.0613 0.0079
7011 AGTACAACTG GGGGGGGGGG 2300837 0.0579 0.0075
7012 GCCGTGAACA GGGGGGGGGG 2057642 0.0518 0.0067
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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: 5.20%
Status: 🔴 FAIL
Reason(s):
Overall undetermined 5.20% >= 5.0%
NTC sample NTC_0001_0001_23KMKGLT4_1 has 3,096,639 reads > 2,000,000
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
Fail file created: ./samplesheet_status.fail
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QC SUMMARY
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Metric Value
Total_Reads 30669874208
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 5.20%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 1
Significant_Unknown_Barcodes 132
High_Mismatch_Barcodes 0
Final_Status FAIL
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QC Analysis completed successfully!
Flowcell Status: FAIL
Reports generated:
- ./qc_report.csv
- ./qc_report_detailed.txt
- ./samplesheet_status.fail
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