A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2020-03-12, 18:03 based on data in:
/beegfs/mk5636/logs/html/H3V73AFX2/merged
General Statistics
Showing 19/19 rows and 3/5 columns.| Sample Name | % Dups | % GC | M Seqs |
|---|---|---|---|
| H3V73AFX2_n01_CD4_CFSE_high | 91.6% | 49% | 0.0 |
| H3V73AFX2_n01_CD4_CFSE_high_corrected | 99.4% | 49% | 9.9 |
| H3V73AFX2_n01_CD4_CFSE_low | 51.3% | 50% | 0.0 |
| H3V73AFX2_n01_CD4_CFSE_low_corrected | 99.4% | 49% | 11.9 |
| H3V73AFX2_n01_CD4_presort | 76.5% | 49% | 0.0 |
| H3V73AFX2_n01_CD4_presort_corrected | 99.4% | 49% | 11.5 |
| H3V73AFX2_n01_CD4_prestim | 90.8% | 49% | 0.0 |
| H3V73AFX2_n01_CD4_prestim_corrected | 99.5% | 49% | 11.6 |
| H3V73AFX2_n01_CD8_CFSE_high | 90.8% | 49% | 0.0 |
| H3V73AFX2_n01_CD8_CFSE_high_corrected | 99.4% | 49% | 9.6 |
| H3V73AFX2_n01_CD8_CFSE_low | 92.8% | 49% | 0.0 |
| H3V73AFX2_n01_CD8_CFSE_low_corrected | 99.4% | 49% | 8.9 |
| H3V73AFX2_n01_CD8_presort | 96.4% | 49% | 0.1 |
| H3V73AFX2_n01_CD8_presort_corrected | 99.4% | 49% | 9.8 |
| H3V73AFX2_n01_CD8_prestim | 78.9% | 49% | 0.0 |
| H3V73AFX2_n01_CD8_prestim_corrected | 99.4% | 49% | 10.0 |
| H3V73AFX2_n01_plasmid | 82.7% | 48% | 0.0 |
| H3V73AFX2_n01_plasmid_corrected | 99.4% | 49% | 8.9 |
| H3V73AFX2_n01_undetermined | 96.2% | 47% | 14.3 |
Demultiplexing Report
Demultiplexing Report
Total Read Count: Total number of PF (Passing Filter) reads in this library.
Portion: The proportion of reads that represent the individual library in the entire Library Pool.
| Sample Name | Total Read Count | Portion (%) |
|---|---|---|
| undetermined_library | 14,323,551 | 13.5 |
| plasmid_corrected | 8,874,429 | 8.3 |
| CD4_prestim_corrected | 11,606,258 | 10.9 |
| CD8_prestim_corrected | 9,963,397 | 9.4 |
| CD4_presort_corrected | 11,485,284 | 10.8 |
| CD8_presort_corrected | 9,803,767 | 9.2 |
| CD4_CFSE_low_corrected | 11,948,325 | 11.2 |
| CD4_CFSE_high_corrected | 9,903,959 | 9.3 |
| CD8_CFSE_low_corrected | 8,873,044 | 8.3 |
| CD8_CFSE_high_corrected | 9,608,928 | 9.0 |
Barcodes of Undetermined Reads
Barcodes of Undetermined Reads
We have determined the barcodes of your undetermined reads (reads containing a barcode that you did not encode in your metadata). Here are the top 20 barcodes belonging to the undetermined reads. The full list is available here.
| Sample Name | Count | Frequency (%) |
|---|---|---|
| GGGGGGGG | 9675321.0 | 67.5 |
| NNNNNNNN | 248867.0 | 1.7 |
| GATCATGA | 121112.0 | 0.8 |
| CTTACCTA | 115763.0 | 0.8 |
| CCTTACTA | 113769.0 | 0.8 |
| CCTACCTA | 102182.0 | 0.7 |
| ACAAGGAA | 94966.0 | 0.7 |
| TGTAACGA | 92359.0 | 0.6 |
| CTTACTTA | 73416.0 | 0.5 |
| ATACCTTA | 66575.0 | 0.5 |
| CGATATGA | 66138.0 | 0.5 |
| ACGCGCGA | 64123.0 | 0.5 |
| ATACTGTA | 63062.0 | 0.4 |
| CGATCAGA | 62037.0 | 0.4 |
| GGTAACGA | 60270.0 | 0.4 |
| ACCAGGAA | 57855.0 | 0.4 |
| ATCGTGTA | 55872.0 | 0.4 |
| GATCTGTA | 52102.0 | 0.4 |
| CATCATGA | 51918.0 | 0.4 |
| CGATCTGA | 48807.0 | 0.3 |
Run Statistics
Run Statistics
Showing 1/1 rows and 4/4 columns.| Sample Name | Total # of Single-End Reads | Total # PF Reads | % Undetermined | % PhiX Aligned |
|---|---|---|---|---|
| 4.0 | 114,604,410 | 106,390,942 | 13.5 | 7.8 |
FastQC
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
Sequence Quality Histograms
The mean quality value across each base position in the read. See the FastQC help.
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.
Click a heatmap row to see a line plot for that dataset.
rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.
Per Base N Content
The percentage of base calls at each position for which an N was called. See the FastQC help.
Sequence Length Distribution
All samples have sequences of a single length (150bp).
Sequence Duplication Levels
The relative level of duplication found for every sequence. See the FastQC help.
Overrepresented sequences
The total amount of overrepresented sequences found in each library. See the FastQC help for further information.
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.
