What Is a Normal No Call Rate in 23andMe Raw Data
A typical no-call rate in 23andMe raw data is usually well under 5%. Here is what no-calls mean and how to check your file in the browser.
No-call rate in 23andMe raw data is usually well under 5%. A no-call is a missing genotype, written as -- in the fourth column. If the file checker reports a no-call rate above the usual expectation, pause and inspect the file before trusting it.
A no-call is missing data, not a failed health result
A 23andMe raw data file is a text file. After the # header lines, each line has rsid, chromosome, position, genotype. A genotype looks like AA, AG, GG, CC, or TT. If the assay does not return a genotype, the genotype column says --. That is a no-call. It is not a result. It is no result.
When people first open the file, they often worry that -- means a deletion or a rare mutation. It doesn't. The assay simply did not return a base pair for that marker. It would be worse if the software filled in a best guess, because downstream tools would then treat the guess as data.
A no-call is missing data, not a variant. The file is telling you it did not get a genotype.
What is a typical no-call rate in 23andMe raw data?
23andMe chip exports are usually well under 5% missing. The rate matters more than the absolute count. A whole-genome VCF has millions of rows and a different expectation than a chip file. A 23andMe v5 file has about 630,000 markers. At 0.5% missing, that is about 3,150 no-calls. At 1% missing, it is about 6,300. Both are ordinary counts.
| No-call rate | Missing markers | How to read it |
|---|---|---|
| 0.1% | about 630 | Illustrative low count |
| 0.5% | about 3,150 | Illustrative typical count |
| 1% | about 6,300 | Illustrative count under the usual expectation |
| 2% | about 12,600 | Illustrative file checker context point |
| 5% | about 31,500 | Illustrative upper context point |
Scroll the table sideways for the rest →
For a v5 file with about 630,000 markers. Numbers are rounded. The third column is illustrative context, not a diagnostic cutoff.
The table gives illustrative rough counts for a v5 file. The 2% and 5% rows are context points, not diagnostic cutoffs.
Why the file has no-calls
A no-call means the assay did not return a genotype for that marker. The raw export records that as --. In a 23andMe file, missing calls are expected at a small rate. The raw data does not say why a given marker is missing, so do not read a no-call cluster as a health finding. If many no-calls appear, a file handling issue is the more likely explanation than a biological cause.
How to check your own file's no-call rate
Drop your 23andMe raw data zip or txt on the free in-browser DNA file checker. It reads the file on your device. It reports the company, chip, genome build, marker count and no-call rate. You do not need to unzip the file first, create an account, or upload anything. The check runs in your browser.
Open the zip exactly as it came from 23andMe. Do not open the text file in Excel and re-save it. Excel changes separators and can make a good file look like it has thousands of extra problems.
What a high no-call rate actually means
A no-call rate above the usual well under 5% expectation is worth pausing over, but it is not a firm cutoff. The file checker reports the rate from the file. In practice, a high no-call rate in 23andMe raw data is usually a file handling issue. Common causes are:
- the PDF or web report instead of the raw data
- a download that stopped early
- a file opened and re-saved in a spreadsheet
- the wrong file or an export from a different tool
If the file is intact and genuinely raw, re-download and inspect it before assuming anything about the sample. The raw file itself does not explain why individual markers are missing.
When a missing marker matters
Most reports skip no-calls. If a specific marker is listed as --, tools either leave the result blank or say 'not determined'. That is not the same as a negative result. For a single-gene check, a missing rsID means you cannot answer that part from this file. If one marker matters to you, open the raw file in a text editor and search the rsID, or check the missing count on the file checker.
The piece people get wrong: a no-call is not a bad result. It is an empty cell. High confidence is not achieved by filling it.
To see what the calls you do have say, the free report at https://healthosx.com/dna reads the same file in the browser, no account and no upload, and walks through the positions it can actually read.
New to raw DNA files? Start with the full guide: How to Download & Analyze Your 23andMe Raw Data Free
Written by
HealthOS Research