Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 72 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 60.92 832178074 1366014682
2 61.17 842927689 1377963340
3 61.31 835568318 1362958509
4 61.19 838334297 1370091080
5 60.88 835687447 1372655984
6 62.06 818564483 1319064061
7 62.10 825030193 1328506662
8 62.21 834796152 1341875953
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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 in the data
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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 31 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6000 CCGTAAGA AGAGTCCA 117286457 8.5860 1.0821
6001 CGACGTTA CTCTGGAT 105543029 7.7263 0.9737
6002 TACGCCTT GCTACTCT 82840621 6.0644 0.7643
6003 CACCTGTT AGGATAGC 81961677 6.0001 0.7562
6004 ATCACACG GTAGCGTA 79449866 5.8162 0.7330
6005 CTTCGACT GATCTTGC 75833483 5.5514 0.6996
6006 AGAACGAG ATTAGCCG 70833887 5.1854 0.6535
6007 TGCTTCCA CGATCGAT 45643447 3.3414 0.4211
6008 ATCACACG GGGGGGGG 8324207 0.6094 0.0768
6009 CGCATGAT GGGGGGGG 8043192 0.5888 0.0742
6010 CTGATCGT GGGGGGGG 7953316 0.5822 0.0734
6011 TGCTTCCA GGGGGGGG 6800066 0.4978 0.0627
6012 AGAACGAG GGGGGGGG 6458814 0.4728 0.0596
6013 CTTGTCGA GGGGGGGG 5688047 0.4164 0.0525
6014 CCGTAAGA GGGGGGGG 5175552 0.3789 0.0477
6015 CGACGTTA CTATGGAT 3026622 0.2216 0.0279
6016 CACCTGTT GGGGGGGG 2637176 0.1931 0.0243
6017 CGACGTTA GGGGGGGG 2303521 0.1686 0.0213
6018 GAGACGAT GGGGGGGG 2024559 0.1482 0.0187
6019 TACGCCTT GGGGGGGG 1434584 0.1050 0.0132
6020 CTTCGACT GGGGGGGG 1429958 0.1047 0.0132
6021 ACTCTCGA GGGGGGGG 1368099 0.1002 0.0126
6022 ATCAAACG GTAGCGTA 1254953 0.0919 0.0116
6023 ACGGAACA GGGGGGGG 1201863 0.0880 0.0111
6024 GGGGGGGG ACCGGTTA 877341 0.0642 0.0081
6025 TTCCAAGG GGGGGGGG 865534 0.0634 0.0080
6026 TGAGCTAG GGGGGGGG 853550 0.0625 0.0079
6027 GGGGGGGG GAACGGTT 780521 0.0571 0.0072
6028 GGGGGGGG CTACAAGG 724306 0.0530 0.0067
6029 GGGGGGGG CGATGTTC 704349 0.0516 0.0065
6030 GGGGGGGG CTCTGGAT 703380 0.0515 0.0065
Lane 2 - Found 30 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 CCGTAAGA AGAGTCCA 118813898 8.6224 1.0962
1 CGACGTTA CTCTGGAT 106651968 7.7398 0.9840
2 TACGCCTT GCTACTCT 84662477 6.1440 0.7811
3 CACCTGTT AGGATAGC 82356640 5.9767 0.7598
4 ATCACACG GTAGCGTA 80588485 5.8484 0.7435
5 CTTCGACT GATCTTGC 77149422 5.5988 0.7118
6 AGAACGAG ATTAGCCG 71969849 5.2229 0.6640
7 TGCTTCCA CGATCGAT 46642422 3.3849 0.4303
8 ATCACACG GGGGGGGG 8390282 0.6089 0.0774
9 CTGATCGT GGGGGGGG 7883196 0.5721 0.0727
10 CGCATGAT GGGGGGGG 7879441 0.5718 0.0727
11 TGCTTCCA GGGGGGGG 6803684 0.4937 0.0628
12 AGAACGAG GGGGGGGG 6560827 0.4761 0.0605
13 CTTGTCGA GGGGGGGG 5647453 0.4098 0.0521
14 CCGTAAGA GGGGGGGG 5433322 0.3943 0.0501
15 CACCTGTT GGGGGGGG 2866919 0.2081 0.0264
16 CGACGTTA CTATGGAT 2768197 0.2009 0.0255
17 CGACGTTA GGGGGGGG 2451016 0.1779 0.0226
18 GAGACGAT GGGGGGGG 2225740 0.1615 0.0205
19 TACGCCTT GGGGGGGG 1545371 0.1121 0.0143
20 CTTCGACT GGGGGGGG 1513819 0.1099 0.0140
21 ACTCTCGA GGGGGGGG 1503114 0.1091 0.0139
22 ACGGAACA GGGGGGGG 1320563 0.0958 0.0122
23 ATCAAACG GTAGCGTA 1168671 0.0848 0.0108
24 TGAGCTAG GGGGGGGG 883541 0.0641 0.0082
25 TTCCAAGG GGGGGGGG 882628 0.0641 0.0081
26 GGGGGGGG ACCGGTTA 879559 0.0638 0.0081
27 GGGGGGGG GAACGGTT 776078 0.0563 0.0072
28 GGGGGGGG CTACAAGG 724328 0.0526 0.0067
29 GGGGGGGG CTCTGGAT 690723 0.0501 0.0064
Lane 3 - Found 31 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1000 CCGTAAGA AGAGTCCA 117192395 8.5984 1.0812
1001 CGACGTTA CTCTGGAT 104031570 7.6328 0.9598
1002 TACGCCTT GCTACTCT 82371500 6.0436 0.7599
1003 CACCTGTT AGGATAGC 80761724 5.9255 0.7451
1004 ATCACACG GTAGCGTA 79911062 5.8631 0.7372
1005 CTTCGACT GATCTTGC 75779521 5.5599 0.6991
1006 AGAACGAG ATTAGCCG 71026579 5.2112 0.6553
1007 TGCTTCCA CGATCGAT 46347182 3.4005 0.4276
1008 ATCACACG GGGGGGGG 8299963 0.6090 0.0766
1009 CGCATGAT GGGGGGGG 7764490 0.5697 0.0716
1010 CTGATCGT GGGGGGGG 7575079 0.5558 0.0699
1011 TGCTTCCA GGGGGGGG 6800790 0.4990 0.0627
1012 CCGTAAGA GGGGGGGG 6673154 0.4896 0.0616
1013 AGAACGAG GGGGGGGG 6407863 0.4701 0.0591
1014 CTTGTCGA GGGGGGGG 5493333 0.4030 0.0507
1015 CACCTGTT GGGGGGGG 3303505 0.2424 0.0305
1016 CGACGTTA CTATGGAT 3164588 0.2322 0.0292
1017 CGACGTTA GGGGGGGG 3001872 0.2202 0.0277
1018 GAGACGAT GGGGGGGG 2688491 0.1973 0.0248
1019 ACTCTCGA GGGGGGGG 1881018 0.1380 0.0174
1020 TACGCCTT GGGGGGGG 1710281 0.1255 0.0158
1021 ACGGAACA GGGGGGGG 1558493 0.1143 0.0144
1022 CTTCGACT GGGGGGGG 1540878 0.1131 0.0142
1023 ATCAAACG GTAGCGTA 1420660 0.1042 0.0131
1024 TGAGCTAG GGGGGGGG 1028319 0.0754 0.0095
1025 TTCCAAGG GGGGGGGG 904706 0.0664 0.0083
1026 GGGGGGGG ACCGGTTA 874808 0.0642 0.0081
1027 GGGGGGGG GAACGGTT 796350 0.0584 0.0073
1028 GGGGGGGG CTACAAGG 738524 0.0542 0.0068
1029 GGGGGGGG CTCTGGAT 686023 0.0503 0.0063
1030 GGGGGGGG CGATGTTC 685335 0.0503 0.0063
Lane 4 - Found 31 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7000 CCGTAAGA AGAGTCCA 117298722 8.5614 1.0822
7001 CGACGTTA CTCTGGAT 104276896 7.6109 0.9620
7002 TACGCCTT GCTACTCT 81753551 5.9670 0.7542
7003 CACCTGTT AGGATAGC 81362787 5.9385 0.7506
7004 ATCACACG GTAGCGTA 80182493 5.8523 0.7398
7005 CTTCGACT GATCTTGC 75743328 5.5283 0.6988
7006 AGAACGAG ATTAGCCG 70981608 5.1808 0.6549
7007 TGCTTCCA CGATCGAT 45888642 3.3493 0.4234
7008 ATCACACG GGGGGGGG 8225318 0.6003 0.0759
7009 CGCATGAT GGGGGGGG 7904156 0.5769 0.0729
7010 CTGATCGT GGGGGGGG 7695271 0.5617 0.0710
7011 CCGTAAGA GGGGGGGG 7292331 0.5323 0.0673
7012 TGCTTCCA GGGGGGGG 6759989 0.4934 0.0624
7013 AGAACGAG GGGGGGGG 6163570 0.4499 0.0569
7014 CTTGTCGA GGGGGGGG 5497542 0.4013 0.0507
7015 CACCTGTT GGGGGGGG 3521085 0.2570 0.0325
7016 CGACGTTA GGGGGGGG 3322114 0.2425 0.0306
7017 CGACGTTA CTATGGAT 3209164 0.2342 0.0296
7018 GAGACGAT GGGGGGGG 2854616 0.2084 0.0263
7019 ACTCTCGA GGGGGGGG 2085139 0.1522 0.0192
7020 TACGCCTT GGGGGGGG 1824244 0.1331 0.0168
7021 ACGGAACA GGGGGGGG 1720165 0.1256 0.0159
7022 CTTCGACT GGGGGGGG 1636339 0.1194 0.0151
7023 ATCAAACG GTAGCGTA 1554354 0.1134 0.0143
7024 TGAGCTAG GGGGGGGG 1190869 0.0869 0.0110
7025 TTCCAAGG GGGGGGGG 1021622 0.0746 0.0094
7026 GGGGGGGG ACCGGTTA 907131 0.0662 0.0084
7027 GGGGGGGG GAACGGTT 838633 0.0612 0.0077
7028 GGGGGGGG CTACAAGG 767949 0.0561 0.0071
7029 GGGGGGGG CGATGTTC 753905 0.0550 0.0070
7030 GGGGGGGG CTCTGGAT 736925 0.0538 0.0068
Lane 5 - Found 29 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2000 CCGTAAGA AGAGTCCA 118909731 8.6627 1.0970
2001 CGACGTTA CTCTGGAT 106377979 7.7498 0.9814
2002 TACGCCTT GCTACTCT 84296525 6.1411 0.7777
2003 CACCTGTT AGGATAGC 81364013 5.9275 0.7507
2004 ATCACACG GTAGCGTA 79872324 5.8188 0.7369
2005 CTTCGACT GATCTTGC 76195522 5.5510 0.7030
2006 AGAACGAG ATTAGCCG 71673238 5.2215 0.6612
2007 TGCTTCCA CGATCGAT 45820738 3.3381 0.4227
2008 ATCACACG GGGGGGGG 7897013 0.5753 0.0729
2009 CGCATGAT GGGGGGGG 7456037 0.5432 0.0688
2010 CTGATCGT GGGGGGGG 7441577 0.5421 0.0687
2011 TGCTTCCA GGGGGGGG 6445077 0.4695 0.0595
2012 AGAACGAG GGGGGGGG 6228991 0.4538 0.0575
2013 CTTGTCGA GGGGGGGG 5439225 0.3963 0.0502
2014 CCGTAAGA GGGGGGGG 5375775 0.3916 0.0496
2015 CGACGTTA CTATGGAT 3061935 0.2231 0.0282
2016 CACCTGTT GGGGGGGG 2748934 0.2003 0.0254
2017 CGACGTTA GGGGGGGG 2430795 0.1771 0.0224
2018 GAGACGAT GGGGGGGG 2230627 0.1625 0.0206
2019 ATCAAACG GTAGCGTA 1553498 0.1132 0.0143
2020 TACGCCTT GGGGGGGG 1491710 0.1087 0.0138
2021 ACTCTCGA GGGGGGGG 1481153 0.1079 0.0137
2022 CTTCGACT GGGGGGGG 1396431 0.1017 0.0129
2023 ACGGAACA GGGGGGGG 1277555 0.0931 0.0118
2024 GGGGGGGG ACCGGTTA 877824 0.0640 0.0081
2025 TGAGCTAG GGGGGGGG 843462 0.0614 0.0078
2026 TTCCAAGG GGGGGGGG 827287 0.0603 0.0076
2027 GGGGGGGG GAACGGTT 774493 0.0564 0.0071
2028 GGGGGGGG CTACAAGG 723221 0.0527 0.0067
Lane 6 - Found 29 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3000 CCGTAAGA AGAGTCCA 114587070 8.6870 1.0572
3001 CGACGTTA CTCTGGAT 100753645 7.6383 0.9295
3002 TACGCCTT GCTACTCT 83961064 6.3652 0.7746
3003 CACCTGTT AGGATAGC 77337253 5.8630 0.7135
3004 ATCACACG GTAGCGTA 76157707 5.7736 0.7026
3005 CTTCGACT GATCTTGC 74936609 5.6810 0.6914
3006 AGAACGAG ATTAGCCG 69660841 5.2811 0.6427
3007 TGCTTCCA CGATCGAT 45698131 3.4644 0.4216
3008 ATCACACG GGGGGGGG 8068677 0.6117 0.0744
3009 CTGATCGT GGGGGGGG 7712413 0.5847 0.0712
3010 CGCATGAT GGGGGGGG 7575313 0.5743 0.0699
3011 TGCTTCCA GGGGGGGG 6842911 0.5188 0.0631
3012 AGAACGAG GGGGGGGG 6434872 0.4878 0.0594
3013 CTTGTCGA GGGGGGGG 5472600 0.4149 0.0505
3014 CCGTAAGA GGGGGGGG 5179369 0.3927 0.0478
3015 CGACGTTA CTATGGAT 3471978 0.2632 0.0320
3016 CACCTGTT GGGGGGGG 2654702 0.2013 0.0245
3017 CGACGTTA GGGGGGGG 2327264 0.1764 0.0215
3018 GAGACGAT GGGGGGGG 1981247 0.1502 0.0183
3019 ATCAAACG GTAGCGTA 1618951 0.1227 0.0149
3020 TACGCCTT GGGGGGGG 1561719 0.1184 0.0144
3021 CTTCGACT GGGGGGGG 1494318 0.1133 0.0138
3022 ACTCTCGA GGGGGGGG 1376335 0.1043 0.0127
3023 ACGGAACA GGGGGGGG 1236738 0.0938 0.0114
3024 TTCCAAGG GGGGGGGG 880561 0.0668 0.0081
3025 TGAGCTAG GGGGGGGG 859558 0.0652 0.0079
3026 GGGGGGGG ACCGGTTA 815348 0.0618 0.0075
3027 GGGGGGGG GAACGGTT 718895 0.0545 0.0066
3028 GGGGGGGG CTACAAGG 660465 0.0501 0.0061
Lane 7 - Found 29 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 CCGTAAGA AGAGTCCA 115428942 8.6886 1.0649
4001 CGACGTTA CTCTGGAT 101680476 7.6537 0.9381
4002 TACGCCTT GCTACTCT 84404186 6.3533 0.7787
4003 CACCTGTT AGGATAGC 78067332 5.8763 0.7202
4004 ATCACACG GTAGCGTA 76953507 5.7925 0.7100
4005 CTTCGACT GATCTTGC 75380533 5.6741 0.6954
4006 AGAACGAG ATTAGCCG 70226278 5.2861 0.6479
4007 TGCTTCCA CGATCGAT 46127135 3.4721 0.4256
4008 ATCACACG GGGGGGGG 8333637 0.6273 0.0769
4009 CTGATCGT GGGGGGGG 8123237 0.6115 0.0749
4010 CGCATGAT GGGGGGGG 7888215 0.5938 0.0728
4011 TGCTTCCA GGGGGGGG 7088833 0.5336 0.0654
4012 AGAACGAG GGGGGGGG 6650653 0.5006 0.0614
4013 CTTGTCGA GGGGGGGG 5687791 0.4281 0.0525
4014 CCGTAAGA GGGGGGGG 5324174 0.4008 0.0491
4015 CGACGTTA CTATGGAT 3309869 0.2491 0.0305
4016 CACCTGTT GGGGGGGG 2633201 0.1982 0.0243
4017 CGACGTTA GGGGGGGG 2362622 0.1778 0.0218
4018 GAGACGAT GGGGGGGG 1977950 0.1489 0.0182
4019 TACGCCTT GGGGGGGG 1550821 0.1167 0.0143
4020 CTTCGACT GGGGGGGG 1483580 0.1117 0.0137
4021 ATCAAACG GTAGCGTA 1456346 0.1096 0.0134
4022 ACTCTCGA GGGGGGGG 1360381 0.1024 0.0126
4023 ACGGAACA GGGGGGGG 1207878 0.0909 0.0111
4024 TTCCAAGG GGGGGGGG 887267 0.0668 0.0082
4025 TGAGCTAG GGGGGGGG 871085 0.0656 0.0080
4026 GGGGGGGG ACCGGTTA 827409 0.0623 0.0076
4027 GGGGGGGG GAACGGTT 731259 0.0550 0.0067
4028 GGGGGGGG CTACAAGG 671918 0.0506 0.0062
Lane 8 - Found 29 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5000 CCGTAAGA AGAGTCCA 116058417 8.6490 1.0707
5001 CGACGTTA CTCTGGAT 102062482 7.6060 0.9416
5002 TACGCCTT GCTACTCT 84350215 6.2860 0.7782
5003 CACCTGTT AGGATAGC 78807251 5.8729 0.7271
5004 ATCACACG GTAGCGTA 77828250 5.8000 0.7180
5005 CTTCGACT GATCTTGC 76205409 5.6790 0.7031
5006 AGAACGAG ATTAGCCG 70906073 5.2841 0.6542
5007 TGCTTCCA CGATCGAT 47055631 3.5067 0.4341
5008 ATCACACG GGGGGGGG 8789770 0.6550 0.0811
5009 CTGATCGT GGGGGGGG 8423371 0.6277 0.0777
5010 CGCATGAT GGGGGGGG 8353623 0.6225 0.0771
5011 TGCTTCCA GGGGGGGG 7510374 0.5597 0.0693
5012 AGAACGAG GGGGGGGG 6950236 0.5179 0.0641
5013 CTTGTCGA GGGGGGGG 5978457 0.4455 0.0552
5014 CCGTAAGA GGGGGGGG 5708152 0.4254 0.0527
5015 CGACGTTA CTATGGAT 3223522 0.2402 0.0297
5016 CACCTGTT GGGGGGGG 2861236 0.2132 0.0264
5017 CGACGTTA GGGGGGGG 2534784 0.1889 0.0234
5018 GAGACGAT GGGGGGGG 2165425 0.1614 0.0200
5019 TACGCCTT GGGGGGGG 1661474 0.1238 0.0153
5020 CTTCGACT GGGGGGGG 1575204 0.1174 0.0145
5021 ACTCTCGA GGGGGGGG 1490466 0.1111 0.0138
5022 ATCAAACG GTAGCGTA 1414034 0.1054 0.0130
5023 ACGGAACA GGGGGGGG 1320769 0.0984 0.0122
5024 TTCCAAGG GGGGGGGG 963716 0.0718 0.0089
5025 TGAGCTAG GGGGGGGG 919509 0.0685 0.0085
5026 GGGGGGGG ACCGGTTA 829726 0.0618 0.0077
5027 GGGGGGGG GAACGGTT 739961 0.0551 0.0068
5028 GGGGGGGG CTACAAGG 688176 0.0513 0.0063
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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: 61.47%
Status: 🔴 FAIL
Reason(s):
Overall undetermined 61.47% > 10.0%
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
Fail file created: ./samplesheet_status.fail
================================================================================
QC SUMMARY
================================================================================
Metric Value
Total_Reads 10839130271
Total_Samples_Analyzed 9
Number_of_Lanes 8
Global_Percent_Undetermined 61.47%
Lanes_Exceeding_Fail_Threshold 1,2,3,4,5,6,7,8
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 0
Significant_Unknown_Barcodes 239
High_Mismatch_Barcodes 0
Final_Status FAIL
================================================================================
QC Analysis completed successfully!
Flowcell Status: FAIL
Reports generated:
- ./qc_report.csv
- ./qc_report_detailed.txt
- ./samplesheet_status.fail
================================================================================