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 6.09 229378957 3765836573
2 6.16 234482693 3808656728
3 6.11 231046869 3782891482
4 6.29 238336927 3786544169
5 6.05 227722125 3766547590
6 6.05 229280588 3789947275
7 6.01 227683499 3790347255
8 6.16 236817895 3841374609
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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 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 TATCCGCG GGGGGGGG 5561254 0.1477 0.0183
2001 GCAATCTG TATTGCGC 5292736 0.1405 0.0174
2002 AGTATCCG ACGAACCA 4945101 0.1313 0.0163
2003 ATGACAGC GGGGGGGG 4653990 0.1236 0.0153
2004 AGATTAGC GGGGGGGG 4532210 0.1204 0.0149
2005 TGGAGATC GGGGGGGG 3513216 0.0933 0.0116
2006 CCAGTCGT GGGGGGGG 3258177 0.0865 0.0107
2007 ACGAGACG GGGGGGGG 3065774 0.0814 0.0101
2008 TAACTTGG GGGGGGGG 2879256 0.0765 0.0095
2009 TCCAACTG GGGGGGGG 2782967 0.0739 0.0092
2010 GCCACCTA GGGGGGGG 2695121 0.0716 0.0089
2011 CAAGACTC GGGGGGGG 2561364 0.0680 0.0084
Lane 2 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 TATCCGCG GGGGGGGG 5587499 0.1467 0.0184
1 GCAATCTG TATTGCGC 5350959 0.1405 0.0176
2 AGTATCCG ACGAACCA 4999677 0.1313 0.0165
3 ATGACAGC GGGGGGGG 4683262 0.1230 0.0154
4 AGATTAGC GGGGGGGG 4524904 0.1188 0.0149
5 TGGAGATC GGGGGGGG 3500694 0.0919 0.0115
6 CCAGTCGT GGGGGGGG 3273832 0.0860 0.0108
7 ACGAGACG GGGGGGGG 3162363 0.0830 0.0104
8 TAACTTGG GGGGGGGG 2878967 0.0756 0.0095
9 TCCAACTG GGGGGGGG 2784587 0.0731 0.0092
10 GCCACCTA GGGGGGGG 2783969 0.0731 0.0092
11 CAAGACTC GGGGGGGG 2501632 0.0657 0.0082
Lane 3 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 TATCCGCG GGGGGGGG 5428364 0.1435 0.0179
6001 GCAATCTG TATTGCGC 5306076 0.1403 0.0175
6002 AGTATCCG ACGAACCA 4978278 0.1316 0.0164
6003 ATGACAGC GGGGGGGG 4552737 0.1204 0.0150
6004 AGATTAGC GGGGGGGG 4415999 0.1167 0.0146
6005 TGGAGATC GGGGGGGG 3405893 0.0900 0.0112
6006 CCAGTCGT GGGGGGGG 3187570 0.0843 0.0105
6007 ACGAGACG GGGGGGGG 3047759 0.0806 0.0100
6008 TAACTTGG GGGGGGGG 2771254 0.0733 0.0091
6009 GCCACCTA GGGGGGGG 2729222 0.0721 0.0090
6010 TCCAACTG GGGGGGGG 2722020 0.0720 0.0090
6011 CAAGACTC GGGGGGGG 2487044 0.0657 0.0082
Lane 4 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 TATCCGCG GGGGGGGG 5461232 0.1442 0.0180
5001 GCAATCTG TATTGCGC 5263065 0.1390 0.0174
5002 AGTATCCG ACGAACCA 4990777 0.1318 0.0165
5003 ATGACAGC GGGGGGGG 4519777 0.1194 0.0149
5004 AGATTAGC GGGGGGGG 4360403 0.1152 0.0144
5005 TGGAGATC GGGGGGGG 3454239 0.0912 0.0114
5006 CCAGTCGT GGGGGGGG 3161379 0.0835 0.0104
5007 ACGAGACG GGGGGGGG 3053585 0.0806 0.0101
5008 GCCACCTA GGGGGGGG 2990106 0.0790 0.0099
5009 TCCAACTG GGGGGGGG 2754590 0.0727 0.0091
5010 TAACTTGG GGGGGGGG 2665030 0.0704 0.0088
5011 CAAGACTC GGGGGGGG 2595123 0.0685 0.0086
5012 ATGTTGCC GGGGGGGG 1920056 0.0507 0.0063
Lane 5 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 TATCCGCG GGGGGGGG 5288258 0.1404 0.0174
4001 GCAATCTG TATTGCGC 5256636 0.1396 0.0173
4002 AGTATCCG ACGAACCA 4969771 0.1319 0.0164
4003 ATGACAGC GGGGGGGG 4438070 0.1178 0.0146
4004 AGATTAGC GGGGGGGG 4317353 0.1146 0.0142
4005 TGGAGATC GGGGGGGG 3291686 0.0874 0.0109
4006 CCAGTCGT GGGGGGGG 3086601 0.0819 0.0102
4007 ACGAGACG GGGGGGGG 2909696 0.0773 0.0096
4008 GCCACCTA GGGGGGGG 2759021 0.0733 0.0091
4009 TAACTTGG GGGGGGGG 2663057 0.0707 0.0088
4010 TCCAACTG GGGGGGGG 2630202 0.0698 0.0087
4011 CAAGACTC GGGGGGGG 2406913 0.0639 0.0079
Lane 6 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 TATCCGCG GGGGGGGG 5430877 0.1433 0.0179
7001 GCAATCTG TATTGCGC 5325134 0.1405 0.0176
7002 AGTATCCG ACGAACCA 4975226 0.1313 0.0164
7003 ATGACAGC GGGGGGGG 4576531 0.1208 0.0151
7004 AGATTAGC GGGGGGGG 4420083 0.1166 0.0146
7005 TGGAGATC GGGGGGGG 3383177 0.0893 0.0112
7006 CCAGTCGT GGGGGGGG 3175152 0.0838 0.0105
7007 ACGAGACG GGGGGGGG 3050980 0.0805 0.0101
7008 TAACTTGG GGGGGGGG 2828666 0.0746 0.0093
7009 GCCACCTA GGGGGGGG 2736101 0.0722 0.0090
7010 TCCAACTG GGGGGGGG 2702717 0.0713 0.0089
7011 CAAGACTC GGGGGGGG 2435310 0.0643 0.0080
Lane 7 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 TATCCGCG GGGGGGGG 5546683 0.1463 0.0183
1001 GCAATCTG TATTGCGC 5333431 0.1407 0.0176
1002 AGTATCCG ACGAACCA 4989930 0.1316 0.0165
1003 ATGACAGC GGGGGGGG 4646297 0.1226 0.0153
1004 AGATTAGC GGGGGGGG 4517094 0.1192 0.0149
1005 TGGAGATC GGGGGGGG 3469002 0.0915 0.0114
1006 CCAGTCGT GGGGGGGG 3257645 0.0859 0.0107
1007 ACGAGACG GGGGGGGG 3135329 0.0827 0.0103
1008 TAACTTGG GGGGGGGG 2885615 0.0761 0.0095
1009 TCCAACTG GGGGGGGG 2769600 0.0731 0.0091
1010 GCCACCTA GGGGGGGG 2715598 0.0716 0.0090
1011 CAAGACTC GGGGGGGG 2517120 0.0664 0.0083
Lane 8 - Found 13 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 TATCCGCG GGGGGGGG 5743487 0.1495 0.0189
3001 GCAATCTG TATTGCGC 5403438 0.1407 0.0178
3002 AGTATCCG ACGAACCA 5064162 0.1318 0.0167
3003 ATGACAGC GGGGGGGG 4789573 0.1247 0.0158
3004 AGATTAGC GGGGGGGG 4650150 0.1211 0.0153
3005 TGGAGATC GGGGGGGG 3573956 0.0930 0.0118
3006 CCAGTCGT GGGGGGGG 3350422 0.0872 0.0110
3007 ACGAGACG GGGGGGGG 3179970 0.0828 0.0105
3008 TAACTTGG GGGGGGGG 2950400 0.0768 0.0097
3009 TCCAACTG GGGGGGGG 2840507 0.0739 0.0094
3010 GCCACCTA GGGGGGGG 2792923 0.0727 0.0092
3011 CAAGACTC GGGGGGGG 2612977 0.0680 0.0086
3012 GAGCAGCT GGGGGGGG 1961492 0.0511 0.0065
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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: 6.11%
Status: 🟡 WARNING
Reason(s):
Overall undetermined 6.11% >= 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 30332145681
Total_Samples_Analyzed 97
Number_of_Lanes 8
Global_Percent_Undetermined 6.11%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 98
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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