Analyzing demux output from: merged Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv Loaded 72 rows from Demultiplex_Stats.csv ================================================================================ 1. % UNDETERMINED PER LANE ================================================================================ 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 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ No samples found with <1000000 reads ================================================================================ 3. NTC SAMPLES WITH >2000000 READS ================================================================================ No NTC samples found in the data ================================================================================ 4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS) ================================================================================ 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 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ No barcodes found with >20.0% mismatch rate ================================================================================ FINAL STATUS CHECK ================================================================================ 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 ================================================================================