Analyzing demux output from: merged
Loading Demultiplex_Stats.csv from: merged/Reports/Demultiplex_Stats.csv
Loaded 388 rows from Demultiplex_Stats.csv
================================================================================
1. % UNDETERMINED PER LANE
================================================================================
Undetermined Summary per Lane:
%_Undetermined Undetermined_Reads Total_Reads
Lane
1 5.22 211346066 4046804284
2 5.33 213604774 4005741146
3 5.18 210105409 4055602240
4 4.90 196957742 4015754163
5 3.56 144447804 4059237853
6 3.75 152658631 4075260777
7 3.85 158180325 4111566941
8 3.87 157368459 4070182884
================================================================================
2. SAMPLES WITH <1000000 READS (NON-NTC)
================================================================================
No samples found with <1000000 reads
================================================================================
3. NTC SAMPLES WITH >2000000 READS
================================================================================
Found 1 NTC samples with >2000000 reads:
SampleID Index # Reads
0 NTC_0001_0001_23LGNLLT4_1 AATTGGCACA-CAGTCGGAGT 3344443
================================================================================
4. TOP UNKNOWN BARCODES (>0.05% OF LANE READS)
================================================================================
Loading Top_Unknown_Barcodes.csv from: merged/Reports/Top_Unknown_Barcodes.csv
Lane 1 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
1001 CCAACTGTAT GGGGGGGGGG 16512354 0.4080 0.0509
1002 GTGACGCACA GGGGGGGGGG 6109919 0.1510 0.0188
1003 GAGTAGTGAC GGGGGGGGGG 5095319 0.1259 0.0157
1004 GATAGGTGAA GGGGGGGGGG 4626452 0.1143 0.0143
1005 AGACGACAGA GGGGGGGGGG 4425791 0.1094 0.0136
1006 TGAGTGTACA GGGGGGGGGG 3787896 0.0936 0.0117
1007 TAGCGAGGCT GGGGGGGGGG 3727400 0.0921 0.0115
1008 AAGGTGTACT GGGGGGGGGG 3677456 0.0909 0.0113
1009 CTCTATACTG GGGGGGGGGG 3616335 0.0894 0.0111
1010 TGTGACGTAT GGGGGGGGGG 3000754 0.0742 0.0093
1011 ACCAGGAATT GGGGGGGGGG 2549661 0.0630 0.0079
1012 TAAGGCTCAC GGGGGGGGGG 2174868 0.0537 0.0067
1013 ATCATACCGC GGGGGGGGGG 2147851 0.0531 0.0066
1014 TCTCCGTACT GGGGGGGGGG 2053900 0.0508 0.0063
Lane 2 - Found 14 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
2001 CCAACTGTAT GGGGGGGGGG 15161678 0.3785 0.0467
2002 GTGACGCACA GGGGGGGGGG 5669869 0.1415 0.0175
2003 GAGTAGTGAC GGGGGGGGGG 5064184 0.1264 0.0156
2004 GATAGGTGAA GGGGGGGGGG 4188170 0.1046 0.0129
2005 AGACGACAGA GGGGGGGGGG 4035783 0.1007 0.0124
2006 TAGCGAGGCT GGGGGGGGGG 3606840 0.0900 0.0111
2007 TGAGTGTACA GGGGGGGGGG 3514278 0.0877 0.0108
2008 AAGGTGTACT GGGGGGGGGG 3471119 0.0867 0.0107
2009 CTCTATACTG GGGGGGGGGG 3427535 0.0856 0.0106
2010 ATCCAGCATG AGATCTCGGT 3346817 0.0836 0.0103
2011 TGTGACGTAT GGGGGGGGGG 2561274 0.0639 0.0079
2012 ACCAGGAATT GGGGGGGGGG 2473783 0.0618 0.0076
2013 ATCATACCGC GGGGGGGGGG 2088118 0.0521 0.0064
2014 TAAGGCTCAC GGGGGGGGGG 2028720 0.0506 0.0063
Lane 3 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
4001 CCAACTGTAT GGGGGGGGGG 15100371 0.3723 0.0465
4002 GTGACGCACA GGGGGGGGGG 5596458 0.1380 0.0173
4003 GAGTAGTGAC GGGGGGGGGG 4917015 0.1212 0.0152
4004 GATAGGTGAA GGGGGGGGGG 4171417 0.1029 0.0129
4005 AGACGACAGA GGGGGGGGGG 3959603 0.0976 0.0122
4006 TGAGTGTACA GGGGGGGGGG 3470378 0.0856 0.0107
4007 TAGCGAGGCT GGGGGGGGGG 3457160 0.0852 0.0107
4008 AAGGTGTACT GGGGGGGGGG 3367739 0.0830 0.0104
4009 CTCTATACTG GGGGGGGGGG 3290240 0.0811 0.0101
4010 ATCCAGCATG AGATCTCGGT 3113478 0.0768 0.0096
4011 TGTGACGTAT GGGGGGGGGG 2514623 0.0620 0.0078
4012 ACCAGGAATT GGGGGGGGGG 2425246 0.0598 0.0075
Lane 4 - Found 12 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
5001 CCAACTGTAT GGGGGGGGGG 14837857 0.3695 0.0457
5002 GTGACGCACA GGGGGGGGGG 5492973 0.1368 0.0169
5003 GAGTAGTGAC GGGGGGGGGG 4397564 0.1095 0.0136
5004 GATAGGTGAA GGGGGGGGGG 4211227 0.1049 0.0130
5005 AGACGACAGA GGGGGGGGGG 3868534 0.0963 0.0119
5006 TGAGTGTACA GGGGGGGGGG 3474004 0.0865 0.0107
5007 TAGCGAGGCT GGGGGGGGGG 3315912 0.0826 0.0102
5008 AAGGTGTACT GGGGGGGGGG 3173047 0.0790 0.0098
5009 CTCTATACTG GGGGGGGGGG 3114019 0.0775 0.0096
5010 TGTGACGTAT GGGGGGGGGG 2835605 0.0706 0.0087
5011 ACCAGGAATT GGGGGGGGGG 2230348 0.0555 0.0069
5012 TAAGGCTCAC GGGGGGGGGG 2041112 0.0508 0.0063
Lane 5 - Found 6 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
6001 TTGGATTGTC GGGGGGGGGG 6386285 0.1573 0.0197
6002 TGCAACACTA GGGGGGGGGG 3653641 0.0900 0.0113
6003 TCGCATGACA GGGGGGGGGG 3506075 0.0864 0.0108
6004 CATCAGGCGT GGGGGGGGGG 3140590 0.0774 0.0097
6005 CCACCTGCTT GGGGGGGGGG 3040546 0.0749 0.0094
6006 CCAGTGCACT GGGGGGGGGG 2445200 0.0602 0.0075
Lane 6 - Found 6 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
7001 TTGGATTGTC GGGGGGGGGG 6897136 0.1692 0.0213
7002 TGCAACACTA GGGGGGGGGG 3977480 0.0976 0.0123
7003 TCGCATGACA GGGGGGGGGG 3856686 0.0946 0.0119
7004 CATCAGGCGT GGGGGGGGGG 3410098 0.0837 0.0105
7005 CCACCTGCTT GGGGGGGGGG 3267007 0.0802 0.0101
7006 CCAGTGCACT GGGGGGGGGG 2652819 0.0651 0.0082
Lane 7 - Found 8 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
3001 TTGGATTGTC GGGGGGGGGG 7196004 0.1750 0.0222
3002 TGCAACACTA GGGGGGGGGG 4140080 0.1007 0.0128
3003 TCGCATGACA GGGGGGGGGG 4133143 0.1005 0.0127
3004 CATCAGGCGT GGGGGGGGGG 3609071 0.0878 0.0111
3005 CCACCTGCTT GGGGGGGGGG 3599203 0.0875 0.0111
3006 CCAGTGCACT GGGGGGGGGG 2744600 0.0668 0.0085
3007 GAAGCAAGCG GGGGGGGGGG 2170074 0.0528 0.0067
3008 ACAATAGCAC GGGGGGGGGG 2116078 0.0515 0.0065
Lane 8 - Found 9 barcodes with >0.05% of lane reads:
index index2 # Reads Percentage_of_Lane Percentage_of_Total
0 TTGGATTGTC GGGGGGGGGG 7535038 0.1851 0.0232
1 TGCAACACTA GGGGGGGGGG 4232194 0.1040 0.0130
2 TCGCATGACA GGGGGGGGGG 4042491 0.0993 0.0125
3 CATCAGGCGT GGGGGGGGGG 3662512 0.0900 0.0113
4 CCACCTGCTT GGGGGGGGGG 3431616 0.0843 0.0106
5 CCAGTGCACT GGGGGGGGGG 2926417 0.0719 0.0090
6 GAAGCAAGCG GGGGGGGGGG 2275317 0.0559 0.0070
7 ACAATAGCAC GGGGGGGGGG 2140678 0.0526 0.0066
8 CGTACTTAGA GGGGGGGGGG 2057009 0.0505 0.0063
================================================================================
5. BARCODES WITH HIGH MISMATCH RATES
================================================================================
No barcodes found with >20.0% mismatch rate
================================================================================
FINAL STATUS CHECK
================================================================================
Overall % Undetermined: 4.45%
Status: 🔴 FAIL
Reason(s):
NTC sample NTC_0001_0001_23LGNLLT4_1 has 3,344,443 reads > 2,000,000
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 32440150288
Total_Samples_Analyzed 96
Number_of_Lanes 8
Global_Percent_Undetermined 4.45%
Lanes_Exceeding_Fail_Threshold None
Samples_with_Low_Reads 0
NTC_Samples_with_High_Reads 1
Significant_Unknown_Barcodes 81
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
================================================================================