Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 392 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 6.80 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
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2. SAMPLES WITH <1000000 READS (NON-NTC)
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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
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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 11 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4000 GATAGGTGAA GGGGGGGGGG 9536564 0.2418 0.0303
4001 GTGACGCACA GGGGGGGGGG 8854352 0.2245 0.0281
4002 TGAGTGTACA GGGGGGGGGG 8433102 0.2138 0.0268
4003 AAGGTGTACT GGGGGGGGGG 7877642 0.1998 0.0250
4004 ATCATACCGC GGGGGGGGGG 4719489 0.1197 0.0150
4005 CTCTATACTG GGGGGGGGGG 4123997 0.1046 0.0131
4006 CCTACTCTGC GGGGGGGGGG 3861447 0.0979 0.0123
4007 TCTCCGTACT GGGGGGGGGG 3505481 0.0889 0.0111
4008 TCGACCAGCA GGGGGGGGGG 3310068 0.0839 0.0105
4009 GCACTACCAG GGGGGGGGGG 2076965 0.0527 0.0066
4010 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
6000 GATAGGTGAA GGGGGGGGGG 9212694 0.2343 0.0292
6001 GTGACGCACA GGGGGGGGGG 8670621 0.2205 0.0275
6002 TGAGTGTACA GGGGGGGGGG 8198443 0.2085 0.0260
6003 AAGGTGTACT GGGGGGGGGG 7805231 0.1985 0.0248
6004 ATCATACCGC GGGGGGGGGG 4799451 0.1220 0.0152
6005 CCTACTCTGC GGGGGGGGGG 4144878 0.1054 0.0132
6006 CTCTATACTG GGGGGGGGGG 4125703 0.1049 0.0131
6007 TCTCCGTACT GGGGGGGGGG 3564323 0.0906 0.0113
6008 TCGACCAGCA GGGGGGGGGG 3379177 0.0859 0.0107
6009 ATCCAGCATG AGATCTCGGT 2704367 0.0688 0.0086
6010 GCACTACCAG GGGGGGGGGG 2024674 0.0515 0.0064
6011 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
0 GATAGGTGAA GGGGGGGGGG 9163090 0.2356 0.0291
1 GTGACGCACA GGGGGGGGGG 8641701 0.2222 0.0274
2 TGAGTGTACA GGGGGGGGGG 8128023 0.2090 0.0258
3 AAGGTGTACT GGGGGGGGGG 7971737 0.2049 0.0253
4 ATCATACCGC GGGGGGGGGG 4756283 0.1223 0.0151
5 CCTACTCTGC GGGGGGGGGG 4168999 0.1072 0.0132
6 CTCTATACTG GGGGGGGGGG 4140416 0.1064 0.0131
7 TCTCCGTACT GGGGGGGGGG 3695847 0.0950 0.0117
8 TCGACCAGCA GGGGGGGGGG 3463055 0.0890 0.0110
9 ATCCAGCATG AGATCTCGGT 2343065 0.0602 0.0074
10 CCAGTATTCT GGGGGGGGGG 2140242 0.0550 0.0068
11 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
1000 GATAGGTGAA GGGGGGGGGG 9072898 0.2347 0.0288
1001 GTGACGCACA GGGGGGGGGG 8906444 0.2304 0.0283
1002 AAGGTGTACT GGGGGGGGGG 8596644 0.2224 0.0273
1003 TGAGTGTACA GGGGGGGGGG 8036447 0.2079 0.0255
1004 ATCATACCGC GGGGGGGGGG 4975903 0.1287 0.0158
1005 CCTACTCTGC GGGGGGGGGG 4517119 0.1169 0.0143
1006 CTCTATACTG GGGGGGGGGG 4401435 0.1139 0.0140
1007 TCTCCGTACT GGGGGGGGGG 4057957 0.1050 0.0129
1008 TCGACCAGCA GGGGGGGGGG 3622473 0.0937 0.0115
1009 CCAGTATTCT GGGGGGGGGG 2487267 0.0643 0.0079
1010 GCACTACCAG GGGGGGGGGG 2408213 0.0623 0.0076
1011 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
2000 GTCGACTCCT GGGGGGGGGG 13563411 0.3439 0.0430
2001 ACAAGAACCT GGGGGGGGGG 7158402 0.1815 0.0227
2002 CACGAGAAGT GGGGGGGGGG 6316072 0.1602 0.0200
2003 ACTTAGATCG GGGGGGGGGG 4668609 0.1184 0.0148
2004 TTGTGAAGGC GGGGGGGGGG 4640329 0.1177 0.0147
2005 TTGCAATGCG GGGGGGGGGG 3858575 0.0978 0.0122
2006 CCTCTGTCAT GGGGGGGGGG 3789823 0.0961 0.0120
2007 ACCTTCGGAC GGGGGGGGGG 3722862 0.0944 0.0118
2008 CATTATCGCT GGGGGGGGGG 3641882 0.0924 0.0116
2009 CTTCGGAATC GGGGGGGGGG 2933468 0.0744 0.0093
2010 AACATAAGGC GGGGGGGGGG 2733174 0.0693 0.0087
2011 GATCAACAAG GGGGGGGGGG 2713155 0.0688 0.0086
2012 CAACCATACA GGGGGGGGGG 2545846 0.0646 0.0081
2013 ACTTCAACAG GGGGGGGGGG 2240273 0.0568 0.0071
2014 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
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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: 6.84%
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
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QC SUMMARY
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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
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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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