> For the complete documentation index, see [llms.txt](https://cmo-ci.gitbook.io/access-quality-control-v2/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://cmo-ci.gitbook.io/access-quality-control-v2/introduction/meta.md).

# Sample meta information

Guide to MultiQC sections displaying sample meta information and pass/fail/warn metrics.

## Introduction

At the top of the MultiQC report are one or two tables showing some per-sample information. One table is for plasma samples and another is for buffy-coat samples; so only one table may show up depending on your sample composition.

![Example MultiQC report showing sample meta information.](https://3106615528-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-MbqIfOAQqfG2kMfi2uM%2Fsync%2F187e5168ba18cba6a2e348dd0eb90e984184b6ad.png?generation=1624468833836129\&alt=media)

## Interpretation

In the above figure you'll notice that most columns are highlighted as either red, yellow or green, which indicates if the metric fails, is borderline, or passes the thresholds set for each, respectively. This allows you to quickly glance at all samples to see where potential issues are. Below are the descriptions for each column and were the data was obtained from.

| Column name         | Source                                                                                                        | Description                                                                                                                               |
| ------------------- | ------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------- |
| cmoSampleName       | LIMS                                                                                                          | The sample name.                                                                                                                          |
| Library input       | LIMS                                                                                                          | The library input.                                                                                                                        |
| Library yield       | LIMS                                                                                                          | The library yield.                                                                                                                        |
| Pool input          | LIMS                                                                                                          | The pool input.                                                                                                                           |
| Raw cov. (pool A)   | MEAN\_TARGET\_COVERAGE column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM, pool A). | The mean sequencing coverage over target regions in Pool A.                                                                               |
| Raw cov. (pool B)   | MEAN\_TARGET\_COVERAGE column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM, pool B). | The mean sequencing coverage over target regions in Pool B.                                                                               |
| Duplex target cov.  | MEAN\_TARGET\_COVERAGE column in the output file produced by GATK-CollectHsMetrics (duplex BAM, pool A).      | Average coverage over pool A targets in the duplex BAM.                                                                                   |
| Minor contamination | [biometrics](https://github.com/msk-access/biometrics)                                                        | Minor contamination based on biometrics.                                                                                                  |
| Major contamination | [biometrics](https://github.com/msk-access/biometrics)                                                        | Major contamination based on.                                                                                                             |
| Fingerprint         | [biometrics](https://github.com/msk-access/biometrics)                                                        | Pass: no unexpected matches/mismatches. NA: if no samples from the same patient to compare with. Fail: has unexpected matches/mismatches. |
| Sex mismatch        | [biometrics](https://github.com/msk-access/biometrics)                                                        | Do the sample's predicted and expected sex mismatch?                                                                                      |
| Ins. size (MODE)    | MODE\_INSERT\_SIZE column from GATK-CollectHsMetrics (Duplex BAM).                                            | The most frequently occurring insert size.                                                                                                |
| N reads             | TOTAL\_READS column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM).                   | Total reads sequenced (uncollapsed)                                                                                                       |
| % Aligned           | PCT\_PF\_UQ\_READS\_ALIGNED column in the output file produced by GATK-CollectHsMetrics (uncollapsed BAM).    | Percentage of reads aligned to the genome.                                                                                                |
| % Noise             | [sequence\_qc](https://github.com/msk-access/sequence_qc)                                                     | Percentage of noise.                                                                                                                      |
| N noise sites       | [sequence\_qc](https://github.com/msk-access/sequence_qc)                                                     | Number of sites contributing to noise.                                                                                                    |