Let’s start by laying out the details you shared to make sure we’re aligned:

• Target SNP: rs6565703
• Linked Gene: DOC2B
• Genomic Position: 12344
• Reported Alleles: A / C
• Web Interface Genotype: A/C (heterozygous)
• JSON Export Genotype: AA (homozygous)

This kind of inconsistency is definitely confusing, so let’s walk through the most likely causes and how to check them:

1. Strand Orientation Mismatch #

23andMe sometimes uses different strand conventions (forward vs. reverse) between their web UI and raw data exports. While your case is AA vs. A/C, it’s worth verifying if the JSON is using the reverse strand. For example, if the web UI shows alleles based on the forward strand, the JSON might list their reverse complements. Check for a strand field in your JSON metadata to confirm the orientation, then cross-reference the alleles against the forward strand reference for rs6565703.

2. Outdated Raw Data Export #

It’s possible you downloaded your JSON file before 23andMe ran a re-analysis of your data or updated their reference genome (like switching from hg19 to hg38). Genotype calls can be revised over time as reference data improves. Check the timestamp on your existing JSON export, then download a fresh copy of your raw data from the 23andMe site and recheck the rs6565703 entry.

3. Parsing or Human Error #

Double-check that you’re looking at the correct SNP in the JSON file—typos happen! Make sure the SNP ID is exactly rs6565703, and confirm the genotype field isn’t being misread (e.g., truncated text, formatting quirks in the JSON structure). Sometimes tools or manual parsing can misinterpret the genotype value, so inspect the raw JSON entry directly.

4. Reach Out to 23andMe Support #

If none of the above fixes the mismatch, this could be an internal data inconsistency on their platform. Contact their support team with specific details: the SNP ID, screenshots of the web UI genotype, the exact JSON entry for the SNP, and timestamps of when you accessed both. Their team can pull your account’s data logs to trace the root cause.

A quick note: Genotype calls aren’t always static—23andMe occasionally updates their analysis pipelines, so small discrepancies between access points can happen as their system improves.

内容的提问来源于stack exchange，提问作者Jimboslice