Analyzing demux output from: merged Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv Loaded 776 rows from Demultiplex_Stats.csv ================================================================================ 1. % UNDETERMINED PER LANE ================================================================================ Undetermined Summary per Lane: %_Undetermined Undetermined_Reads Total_Reads Lane 1 6.80 256076560 3764221011 2 6.68 249916067 3743254453 3 6.99 259502348 3713846173 4 7.39 273892746 3706675031 5 7.41 272345315 3676440007 6 6.76 254194919 3761057280 7 6.56 248021330 3778753744 8 6.78 255971636 3774977755 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ Found 1 samples with <1000000 reads: SampleID ... Lane(s) 20 1173_FWA_T1_RNA_SLD_01_A23T55JLT4_2 ... 1,2,3,4,5,6,7,8 [1 rows x 4 columns] ================================================================================ 3. NTC SAMPLES WITH >2000000 READS ================================================================================ No NTC samples found with >2000000 reads ================================================================================ 4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS) ================================================================================ Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv Lane 1 - Found 16 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 ACCAGGAATT GGGGGGGGGG 5754910 0.1529 0.0192 1 AGCCTCTGCT GGGGGGGGGG 5445921 0.1447 0.0182 2 GTGACGCACA GGGGGGGGGG 4425130 0.1176 0.0148 3 AGACGACAGA GGGGGGGGGG 4040373 0.1073 0.0135 4 ACTCGTCCAG GGGGGGGGGG 3980549 0.1057 0.0133 5 GAGTAGTGAC GGGGGGGGGG 3951009 0.1050 0.0132 6 TGGCACTGAT GGGGGGGGGG 3799569 0.1009 0.0127 7 TGAGTGTACA GGGGGGGGGG 3752965 0.0997 0.0125 8 GCATTCCTTC GGGGGGGGGG 3283868 0.0872 0.0110 9 CTCTATACTG GGGGGGGGGG 3041321 0.0808 0.0102 10 TCTCCGTACT GGGGGGGGGG 3040129 0.0808 0.0102 11 GCAGAAGTCT GGGGGGGGGG 2817544 0.0749 0.0094 12 GATAGGTGAA GGGGGGGGGG 2737065 0.0727 0.0091 13 TAGCGAGGCT GGGGGGGGGG 2362509 0.0628 0.0079 14 TCACCGTGGT GGGGGGGGGG 2201252 0.0585 0.0074 15 TTGCCGTATC GGGGGGGGGG 2026053 0.0538 0.0068 Lane 2 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3000 ACCAGGAATT GGGGGGGGGG 5518342 0.1474 0.0184 3001 AGCCTCTGCT GGGGGGGGGG 5198858 0.1389 0.0174 3002 GTGACGCACA GGGGGGGGGG 4256841 0.1137 0.0142 3003 AGACGACAGA GGGGGGGGGG 3913329 0.1045 0.0131 3004 ACTCGTCCAG GGGGGGGGGG 3823855 0.1022 0.0128 3005 GAGTAGTGAC GGGGGGGGGG 3744352 0.1000 0.0125 3006 TGGCACTGAT GGGGGGGGGG 3700076 0.0988 0.0124 3007 TGAGTGTACA GGGGGGGGGG 3651655 0.0976 0.0122 3008 GCATTCCTTC GGGGGGGGGG 3240950 0.0866 0.0108 3009 TCTCCGTACT GGGGGGGGGG 2966452 0.0792 0.0099 3010 CTCTATACTG GGGGGGGGGG 2943543 0.0786 0.0098 3011 GCAGAAGTCT GGGGGGGGGG 2749993 0.0735 0.0092 3012 GATAGGTGAA GGGGGGGGGG 2643038 0.0706 0.0088 3013 TAGCGAGGCT GGGGGGGGGG 2293719 0.0613 0.0077 3014 TCACCGTGGT GGGGGGGGGG 2152967 0.0575 0.0072 Lane 3 - Found 17 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5000 ACCAGGAATT GGGGGGGGGG 5754547 0.1549 0.0192 5001 AGCCTCTGCT GGGGGGGGGG 4996013 0.1345 0.0167 5002 GTGACGCACA GGGGGGGGGG 4234808 0.1140 0.0142 5003 ACTCGTCCAG GGGGGGGGGG 4047358 0.1090 0.0135 5004 TGGCACTGAT GGGGGGGGGG 3884212 0.1046 0.0130 5005 GAGTAGTGAC GGGGGGGGGG 3867643 0.1041 0.0129 5006 AGACGACAGA GGGGGGGGGG 3734697 0.1006 0.0125 5007 TGAGTGTACA GGGGGGGGGG 3561319 0.0959 0.0119 5008 TCTCCGTACT GGGGGGGGGG 3318618 0.0894 0.0111 5009 GCATTCCTTC GGGGGGGGGG 3040510 0.0819 0.0102 5010 CTCTATACTG GGGGGGGGGG 3035642 0.0817 0.0101 5011 GCAGAAGTCT GGGGGGGGGG 2839537 0.0765 0.0095 5012 TAGCGAGGCT GGGGGGGGGG 2537684 0.0683 0.0085 5013 GATAGGTGAA GGGGGGGGGG 2518457 0.0678 0.0084 5014 TTGCCGTATC GGGGGGGGGG 2328594 0.0627 0.0078 5015 TCACCGTGGT GGGGGGGGGG 2088619 0.0562 0.0070 5016 GCACTACCAG GGGGGGGGGG 1863200 0.0502 0.0062 Lane 4 - Found 19 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1000 ACCAGGAATT GGGGGGGGGG 5935969 0.1601 0.0198 1001 AGCCTCTGCT GGGGGGGGGG 5005206 0.1350 0.0167 1002 GTGACGCACA GGGGGGGGGG 4314983 0.1164 0.0144 1003 TGGCACTGAT GGGGGGGGGG 4168021 0.1124 0.0139 1004 ACTCGTCCAG GGGGGGGGGG 4116275 0.1111 0.0138 1005 GAGTAGTGAC GGGGGGGGGG 3871275 0.1044 0.0129 1006 AGACGACAGA GGGGGGGGGG 3754763 0.1013 0.0125 1007 TGAGTGTACA GGGGGGGGGG 3578641 0.0965 0.0120 1008 TCTCCGTACT GGGGGGGGGG 3528687 0.0952 0.0118 1009 CTCTATACTG GGGGGGGGGG 3155066 0.0851 0.0105 1010 GCAGAAGTCT GGGGGGGGGG 3056289 0.0825 0.0102 1011 GCATTCCTTC GGGGGGGGGG 2992824 0.0807 0.0100 1012 TAGCGAGGCT GGGGGGGGGG 2672706 0.0721 0.0089 1013 GATAGGTGAA GGGGGGGGGG 2533806 0.0684 0.0085 1014 TTGCCGTATC GGGGGGGGGG 2429398 0.0655 0.0081 1015 GCACTACCAG GGGGGGGGGG 2169800 0.0585 0.0073 1016 GATTGGCGAT GGGGGGGGGG 2137471 0.0577 0.0071 1017 CCACTCAACG GGGGGGGGGG 2091394 0.0564 0.0070 1018 TCACCGTGGT GGGGGGGGGG 2055667 0.0555 0.0069 Lane 5 - Found 20 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2000 ACCAGGAATT GGGGGGGGGG 5823993 0.1584 0.0195 2001 AGCCTCTGCT GGGGGGGGGG 4820673 0.1311 0.0161 2002 GTGACGCACA GGGGGGGGGG 4228057 0.1150 0.0141 2003 ACTCGTCCAG GGGGGGGGGG 4045505 0.1100 0.0135 2004 TGGCACTGAT GGGGGGGGGG 4005573 0.1090 0.0134 2005 GAGTAGTGAC GGGGGGGGGG 3860216 0.1050 0.0129 2006 AGACGACAGA GGGGGGGGGG 3615673 0.0983 0.0121 2007 TGAGTGTACA GGGGGGGGGG 3582225 0.0974 0.0120 2008 TCTCCGTACT GGGGGGGGGG 3414616 0.0929 0.0114 2009 CTCTATACTG GGGGGGGGGG 3049855 0.0830 0.0102 2010 GCATTCCTTC GGGGGGGGGG 2998867 0.0816 0.0100 2011 GCAGAAGTCT GGGGGGGGGG 2879936 0.0783 0.0096 2012 TAGCGAGGCT GGGGGGGGGG 2639442 0.0718 0.0088 2013 TTGCCGTATC GGGGGGGGGG 2633074 0.0716 0.0088 2014 GATAGGTGAA GGGGGGGGGG 2474170 0.0673 0.0083 2015 TCACCGTGGT GGGGGGGGGG 2083146 0.0567 0.0070 2016 GCACTACCAG GGGGGGGGGG 2012157 0.0547 0.0067 2017 GATTGGCGAT GGGGGGGGGG 1971375 0.0536 0.0066 2018 ATCCAGCATG AGATCTCGGT 1921932 0.0523 0.0064 2019 CCACTCAACG GGGGGGGGGG 1920206 0.0522 0.0064 Lane 6 - Found 16 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6000 ACCAGGAATT GGGGGGGGGG 5700301 0.1516 0.0191 6001 AGCCTCTGCT GGGGGGGGGG 5081395 0.1351 0.0170 6002 GTGACGCACA GGGGGGGGGG 4214886 0.1121 0.0141 6003 ACTCGTCCAG GGGGGGGGGG 3980604 0.1058 0.0133 6004 GAGTAGTGAC GGGGGGGGGG 3840003 0.1021 0.0128 6005 TGGCACTGAT GGGGGGGGGG 3814600 0.1014 0.0127 6006 AGACGACAGA GGGGGGGGGG 3792318 0.1008 0.0127 6007 TGAGTGTACA GGGGGGGGGG 3575856 0.0951 0.0120 6008 TCTCCGTACT GGGGGGGGGG 3153155 0.0838 0.0105 6009 GCATTCCTTC GGGGGGGGGG 3128472 0.0832 0.0105 6010 CTCTATACTG GGGGGGGGGG 2997077 0.0797 0.0100 6011 GCAGAAGTCT GGGGGGGGGG 2783276 0.0740 0.0093 6012 GATAGGTGAA GGGGGGGGGG 2561031 0.0681 0.0086 6013 TAGCGAGGCT GGGGGGGGGG 2413183 0.0642 0.0081 6014 TCACCGTGGT GGGGGGGGGG 2104264 0.0559 0.0070 6015 TTGCCGTATC GGGGGGGGGG 2068331 0.0550 0.0069 Lane 7 - Found 17 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7000 ACCAGGAATT GGGGGGGGGG 5604199 0.1483 0.0187 7001 AGCCTCTGCT GGGGGGGGGG 5271769 0.1395 0.0176 7002 GTGACGCACA GGGGGGGGGG 4296770 0.1137 0.0144 7003 AGACGACAGA GGGGGGGGGG 3894373 0.1031 0.0130 7004 ACTCGTCCAG GGGGGGGGGG 3883331 0.1028 0.0130 7005 GAGTAGTGAC GGGGGGGGGG 3841180 0.1017 0.0128 7006 TGGCACTGAT GGGGGGGGGG 3683893 0.0975 0.0123 7007 TGAGTGTACA GGGGGGGGGG 3617051 0.0957 0.0121 7008 GCATTCCTTC GGGGGGGGGG 3155024 0.0835 0.0105 7009 TCTCCGTACT GGGGGGGGGG 2973204 0.0787 0.0099 7010 CTCTATACTG GGGGGGGGGG 2957480 0.0783 0.0099 7011 GCAGAAGTCT GGGGGGGGGG 2715372 0.0719 0.0091 7012 GATAGGTGAA GGGGGGGGGG 2626419 0.0695 0.0088 7013 TAGCGAGGCT GGGGGGGGGG 2293063 0.0607 0.0077 7014 TCACCGTGGT GGGGGGGGGG 2117939 0.0560 0.0071 7015 TTGCCGTATC GGGGGGGGGG 1993122 0.0527 0.0067 7016 ATCCAGCATG AGATCTCGGT 1901800 0.0503 0.0064 Lane 8 - Found 16 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4000 ACCAGGAATT GGGGGGGGGG 5695957 0.1509 0.0190 4001 AGCCTCTGCT GGGGGGGGGG 5401826 0.1431 0.0181 4002 GTGACGCACA GGGGGGGGGG 4334850 0.1148 0.0145 4003 AGACGACAGA GGGGGGGGGG 4005933 0.1061 0.0134 4004 ACTCGTCCAG GGGGGGGGGG 3993991 0.1058 0.0133 4005 GAGTAGTGAC GGGGGGGGGG 3856942 0.1022 0.0129 4006 TGGCACTGAT GGGGGGGGGG 3766465 0.0998 0.0126 4007 TGAGTGTACA GGGGGGGGGG 3693635 0.0978 0.0123 4008 GCATTCCTTC GGGGGGGGGG 3227519 0.0855 0.0108 4009 TCTCCGTACT GGGGGGGGGG 3060307 0.0811 0.0102 4010 CTCTATACTG GGGGGGGGGG 3024366 0.0801 0.0101 4011 GCAGAAGTCT GGGGGGGGGG 2817806 0.0746 0.0094 4012 GATAGGTGAA GGGGGGGGGG 2667562 0.0707 0.0089 4013 TAGCGAGGCT GGGGGGGGGG 2333333 0.0618 0.0078 4014 TCACCGTGGT GGGGGGGGGG 2168604 0.0574 0.0072 4015 TTGCCGTATC GGGGGGGGGG 1955813 0.0518 0.0065 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ ⚠️ WARNING: 4 sample(s) with >20.0% mismatch rate: Lane SampleID ... # Reads Mismatch_Rate 273 5 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 29720632 21.36 176 4 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 29694497 20.36 661 6 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 30796012 20.07 564 3 1173_QJL_T1_RNA_SLD_01_A23T55JLT4_2 ... 30230749 20.01 [4 rows x 5 columns] Mismatch Rate Summary: Average mismatch rate: 2.55% Maximum mismatch rate: 21.36% Samples with >20.0% mismatch: 4 ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 6.92% Status: 🟡 WARNING Reason(s): Overall undetermined 6.92% >= 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 ================================================================================ QC SUMMARY ================================================================================ Metric Value Total_Reads 29919225454 Total_Samples_Analyzed 97 Number_of_Lanes 8 Global_Percent_Undetermined 6.92% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 1 NTC_Samples_with_High_Reads 0 Significant_Unknown_Barcodes 136 High_Mismatch_Barcodes 4 Final_Status WARNING ================================================================================ QC Analysis completed successfully! Flowcell Status: WARNING Reports generated: - ./qc_report.csv - ./qc_report_detailed.txt - ./samplesheet_status.warning ================================================================================