Analyzing demux output from: merged Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv Loaded 392 rows from Demultiplex_Stats.csv ================================================================================ 1. % UNDETERMINED PER LANE ================================================================================ Undetermined Summary per Lane: %_Undetermined Undetermined_Reads Total_Reads Lane 1 6.80 268308801 3943473605 2 6.81 267758180 3932731736 3 6.99 271863886 3889634474 4 7.33 283228840 3865350905 5 6.77 266843082 3943517784 6 6.76 266199678 3935511793 7 6.65 265625658 3994328926 8 6.64 265680856 4002815434 ================================================================================ 2. SAMPLES WITH <1000000 READS (NON-NTC) ================================================================================ Found 17 samples with <1000000 reads: SampleID Index # Reads Lane(s) 65 659_dkd-T1-TRNA-1_B23MHV2LT4_1 AGACGACAGA-GAGCTGGAAT 184741 1,2,3,4 50 659_cuO-T1-TRNA-1_B23MHV2LT4_1 TTCTACCGGC-TACTCGTAAG 192558 5,6,7,8 77 659_egp-T1-TRNA-1_B23MHV2LT4_1 GCCAAGTAAC-TGCGTGATGA 197292 5,6,7,8 76 659_eeB-T1-TRNA-1_B23MHV2LT4_1 CACGTAAGAG-TCAATCCGCG 205713 5,6,7,8 69 659_e0S-T1-TRNA-1_B23MHV2LT4_1 GCTACAGGTC-TTATGCAGGA 233173 5,6,7,8 2 659_8h-T1-TRNA-1_B23MHV2LT4_1 TAAGGCTCAC-GACGTTACTT 285607 1,2,3,4 49 659_cq5-T1-TRNA-1_B23MHV2LT4_1 TGCTTCCAAG-CAGATGTTAC 292068 1,2,3,4 33 659_buj-T1-TRNA-1_B23MHV2LT4_1 AATCGAACTC-ACGAACCTTA 319430 5,6,7,8 35 659_cAa-T1-TRNA-1_B23MHV2LT4_1 CCAACTGTAT-GCGCTAGAGA 332597 1,2,3,4 58 659_dQk-T1-TRNA-1_B23MHV2LT4_1 AGAGTATGTG-AGATGGCTTC 353103 5,6,7,8 12 659_Wm-T1-TRNA-1_B23MHV2LT4_1 GCAGATGTAA-TACACGCCTC 364298 5,6,7,8 54 659_d0V-T1-TRNA-1_B23MHV2LT4_1 ACCAGGAATT-AGCATGGCAT 367467 1,2,3,4 53 659_d0M-T1-TRNA-1_B23MHV2LT4_1 CAATGCGTGT-ATGTTCGCGC 395877 1,2,3,4 72 659_eKx-T1-TRNA-1_B23MHV2LT4_1 CATATGGTGC-ACAGATCTCA 397977 1,2,3,4 14 659_b6o-T1-TRNA-1_B23MHV2LT4_1 TAGCGAGGCT-TTGCTCACGG 437890 1,2,3,4 10 659_R1-T1-TRNA-1_B23MHV2LT4_1 TGTCAGGCTT-GATTCCTTAC 500047 1,2,3,4 68 659_dwi-T1-TRNA-1_B23MHV2LT4_1 TGTGACGTAT-GCAGCGTTAG 543963 1,2,3,4 ================================================================================ 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 11 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 2000 GATAGGTGAA GGGGGGGGGG 9536564 0.2418 0.0303 2001 GTGACGCACA GGGGGGGGGG 8854352 0.2245 0.0281 2002 TGAGTGTACA GGGGGGGGGG 8433102 0.2138 0.0268 2003 AAGGTGTACT GGGGGGGGGG 7877642 0.1998 0.0250 2004 ATCATACCGC GGGGGGGGGG 4719489 0.1197 0.0150 2005 CTCTATACTG GGGGGGGGGG 4123997 0.1046 0.0131 2006 CCTACTCTGC GGGGGGGGGG 3861447 0.0979 0.0123 2007 TCTCCGTACT GGGGGGGGGG 3505481 0.0889 0.0111 2008 TCGACCAGCA GGGGGGGGGG 3310068 0.0839 0.0105 2009 GCACTACCAG GGGGGGGGGG 2076965 0.0527 0.0066 2010 CCAGTATTCT GGGGGGGGGG 2026912 0.0514 0.0064 Lane 2 - Found 12 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 1000 GATAGGTGAA GGGGGGGGGG 9212694 0.2343 0.0292 1001 GTGACGCACA GGGGGGGGGG 8670621 0.2205 0.0275 1002 TGAGTGTACA GGGGGGGGGG 8198443 0.2085 0.0260 1003 AAGGTGTACT GGGGGGGGGG 7805231 0.1985 0.0248 1004 ATCATACCGC GGGGGGGGGG 4799451 0.1220 0.0152 1005 CCTACTCTGC GGGGGGGGGG 4144878 0.1054 0.0132 1006 CTCTATACTG GGGGGGGGGG 4125703 0.1049 0.0131 1007 TCTCCGTACT GGGGGGGGGG 3564323 0.0906 0.0113 1008 TCGACCAGCA GGGGGGGGGG 3379177 0.0859 0.0107 1009 ATCCAGCATG AGATCTCGGT 2704367 0.0688 0.0086 1010 GCACTACCAG GGGGGGGGGG 2024674 0.0515 0.0064 1011 CCAGTATTCT GGGGGGGGGG 2015291 0.0512 0.0064 Lane 3 - Found 12 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 6000 GATAGGTGAA GGGGGGGGGG 9163090 0.2356 0.0291 6001 GTGACGCACA GGGGGGGGGG 8641701 0.2222 0.0274 6002 TGAGTGTACA GGGGGGGGGG 8128023 0.2090 0.0258 6003 AAGGTGTACT GGGGGGGGGG 7971737 0.2049 0.0253 6004 ATCATACCGC GGGGGGGGGG 4756283 0.1223 0.0151 6005 CCTACTCTGC GGGGGGGGGG 4168999 0.1072 0.0132 6006 CTCTATACTG GGGGGGGGGG 4140416 0.1064 0.0131 6007 TCTCCGTACT GGGGGGGGGG 3695847 0.0950 0.0117 6008 TCGACCAGCA GGGGGGGGGG 3463055 0.0890 0.0110 6009 ATCCAGCATG AGATCTCGGT 2343065 0.0602 0.0074 6010 CCAGTATTCT GGGGGGGGGG 2140242 0.0550 0.0068 6011 GCACTACCAG GGGGGGGGGG 2128689 0.0547 0.0068 Lane 4 - Found 12 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 0 GATAGGTGAA GGGGGGGGGG 9072898 0.2347 0.0288 1 GTGACGCACA GGGGGGGGGG 8906444 0.2304 0.0283 2 AAGGTGTACT GGGGGGGGGG 8596644 0.2224 0.0273 3 TGAGTGTACA GGGGGGGGGG 8036447 0.2079 0.0255 4 ATCATACCGC GGGGGGGGGG 4975903 0.1287 0.0158 5 CCTACTCTGC GGGGGGGGGG 4517119 0.1169 0.0143 6 CTCTATACTG GGGGGGGGGG 4401435 0.1139 0.0140 7 TCTCCGTACT GGGGGGGGGG 4057957 0.1050 0.0129 8 TCGACCAGCA GGGGGGGGGG 3622473 0.0937 0.0115 9 CCAGTATTCT GGGGGGGGGG 2487267 0.0643 0.0079 10 GCACTACCAG GGGGGGGGGG 2408213 0.0623 0.0076 11 ATCCAGCATG AGATCTCGGT 2154935 0.0558 0.0068 Lane 5 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 4000 GTCGACTCCT GGGGGGGGGG 13563411 0.3439 0.0430 4001 ACAAGAACCT GGGGGGGGGG 7158402 0.1815 0.0227 4002 CACGAGAAGT GGGGGGGGGG 6316072 0.1602 0.0200 4003 ACTTAGATCG GGGGGGGGGG 4668609 0.1184 0.0148 4004 TTGTGAAGGC GGGGGGGGGG 4640329 0.1177 0.0147 4005 TTGCAATGCG GGGGGGGGGG 3858575 0.0978 0.0122 4006 CCTCTGTCAT GGGGGGGGGG 3789823 0.0961 0.0120 4007 ACCTTCGGAC GGGGGGGGGG 3722862 0.0944 0.0118 4008 CATTATCGCT GGGGGGGGGG 3641882 0.0924 0.0116 4009 CTTCGGAATC GGGGGGGGGG 2933468 0.0744 0.0093 4010 AACATAAGGC GGGGGGGGGG 2733174 0.0693 0.0087 4011 GATCAACAAG GGGGGGGGGG 2713155 0.0688 0.0086 4012 CAACCATACA GGGGGGGGGG 2545846 0.0646 0.0081 4013 ACTTCAACAG GGGGGGGGGG 2240273 0.0568 0.0071 4014 CGGATTGATC GGGGGGGGGG 2103137 0.0533 0.0067 Lane 6 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 5000 GTCGACTCCT GGGGGGGGGG 14936519 0.3795 0.0474 5001 ACAAGAACCT GGGGGGGGGG 6972116 0.1772 0.0221 5002 CACGAGAAGT GGGGGGGGGG 6526625 0.1658 0.0207 5003 TTGTGAAGGC GGGGGGGGGG 4810088 0.1222 0.0153 5004 ACTTAGATCG GGGGGGGGGG 4627079 0.1176 0.0147 5005 ACCTTCGGAC GGGGGGGGGG 3929895 0.0999 0.0125 5006 CCTCTGTCAT GGGGGGGGGG 3840607 0.0976 0.0122 5007 TTGCAATGCG GGGGGGGGGG 3757990 0.0955 0.0119 5008 CATTATCGCT GGGGGGGGGG 3756470 0.0955 0.0119 5009 CTTCGGAATC GGGGGGGGGG 3112078 0.0791 0.0099 5010 GATCAACAAG GGGGGGGGGG 2677814 0.0680 0.0085 5011 AACATAAGGC GGGGGGGGGG 2608361 0.0663 0.0083 5012 CAACCATACA GGGGGGGGGG 2389463 0.0607 0.0076 5013 ACTTCAACAG GGGGGGGGGG 2038223 0.0518 0.0065 5014 CGGATTGATC GGGGGGGGGG 2032622 0.0516 0.0065 Lane 7 - Found 15 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 7000 GTCGACTCCT GGGGGGGGGG 15103196 0.3781 0.0479 7001 ACAAGAACCT GGGGGGGGGG 7261921 0.1818 0.0230 7002 CACGAGAAGT GGGGGGGGGG 6652969 0.1666 0.0211 7003 TTGTGAAGGC GGGGGGGGGG 4948886 0.1239 0.0157 7004 ACTTAGATCG GGGGGGGGGG 4800964 0.1202 0.0152 7005 ACCTTCGGAC GGGGGGGGGG 4026177 0.1008 0.0128 7006 CCTCTGTCAT GGGGGGGGGG 3900419 0.0976 0.0124 7007 TTGCAATGCG GGGGGGGGGG 3892184 0.0974 0.0124 7008 CATTATCGCT GGGGGGGGGG 3855487 0.0965 0.0122 7009 CTTCGGAATC GGGGGGGGGG 3114668 0.0780 0.0099 7010 GATCAACAAG GGGGGGGGGG 2770660 0.0694 0.0088 7011 AACATAAGGC GGGGGGGGGG 2735297 0.0685 0.0087 7012 CAACCATACA GGGGGGGGGG 2476809 0.0620 0.0079 7013 ACTTCAACAG GGGGGGGGGG 2131175 0.0534 0.0068 7014 CGGATTGATC GGGGGGGGGG 2130566 0.0533 0.0068 Lane 8 - Found 14 barcodes with >0.05% of lane reads: index index2 # Reads Percentage_of_Lane Percentage_of_Total 3000 GTCGACTCCT GGGGGGGGGG 15533349 0.3881 0.0493 3001 ACAAGAACCT GGGGGGGGGG 7270640 0.1816 0.0231 3002 CACGAGAAGT GGGGGGGGGG 6913650 0.1727 0.0219 3003 TTGTGAAGGC GGGGGGGGGG 5231938 0.1307 0.0166 3004 ACTTAGATCG GGGGGGGGGG 4830318 0.1207 0.0153 3005 ACCTTCGGAC GGGGGGGGGG 4053719 0.1013 0.0129 3006 CCTCTGTCAT GGGGGGGGGG 3999048 0.0999 0.0127 3007 TTGCAATGCG GGGGGGGGGG 3962933 0.0990 0.0126 3008 CATTATCGCT GGGGGGGGGG 3819692 0.0954 0.0121 3009 CTTCGGAATC GGGGGGGGGG 3232535 0.0808 0.0103 3010 GATCAACAAG GGGGGGGGGG 2743122 0.0685 0.0087 3011 AACATAAGGC GGGGGGGGGG 2706867 0.0676 0.0086 3012 CAACCATACA GGGGGGGGGG 2366508 0.0591 0.0075 3013 CGGATTGATC GGGGGGGGGG 2065660 0.0516 0.0066 ================================================================================ 5. BARCODES WITH HIGH MISMATCH RATES ================================================================================ No barcodes found with >20.0% mismatch rate ================================================================================ FINAL STATUS CHECK ================================================================================ Overall % Undetermined: 6.84% Status: 🟡 WARNING Reason(s): Overall undetermined 6.84% >= 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 31507364657 Total_Samples_Analyzed 97 Number_of_Lanes 8 Global_Percent_Undetermined 6.84% Lanes_Exceeding_Fail_Threshold None Samples_with_Low_Reads 17 NTC_Samples_with_High_Reads 0 Significant_Unknown_Barcodes 106 High_Mismatch_Barcodes 0 Final_Status WARNING ================================================================================ QC Analysis completed successfully! Flowcell Status: WARNING Reports generated: - ./qc_report.csv - ./qc_report_detailed.txt - ./samplesheet_status.warning ================================================================================