Read your report
Coverage and callability: why your file type changes what we can say
Two people with the same DNA can get very different reports from Aimosti. The difference is not the genome, it is the file they uploaded, and what that file lets us read.
The claim. If my report does not list a gene, a variant, or a risk, that means I was checked and I am clear. A result is a result, whatever file I uploaded.
Verdict. What a report can say is bounded by the file you uploaded. A genotyping chip, a whole-genome file, and aligned reads each let us read different things, and on every file type an absence can mean 'examined and clear' or simply 'never looked there'. We label which one it is, and we never read a blank as a clean bill of health.
A genome report is a reading of a file, not of your body, and different files expose different parts of your DNA. A genotyping chip measures a fixed list of common positions. A whole-genome file, usually a gVCF, can read far more and also records which regions were covered confidently. Aligned reads let a gene be re-examined base by base. Because of this, the same DNA can produce a narrower or a wider report depending only on the file, and on every file type a missing entry can mean the position was read and matched the reference, or that it was never covered at all.
First, what a 'file' is
Aimosti never sequences your DNA. You upload a file from a service that already did, and the report is only as wide as that file allows. Three kinds of file behave very differently.
A genotyping chip, also called an array, is the file behind most consumer ancestry kits. It reads a fixed, pre-chosen list of common positions across the genome and reports your letter at each one. It is reliable for what it was built to test: pharmacogenomics, polygenic scores, traits, ancestry, and a handful of well-characterised single-gene findings such as APOE, HFE, Lp(a) and ABO. It says nothing about the positions it was never designed to probe.
A whole-genome file, usually delivered as a gVCF, comes from sequencing rather than an array. It can in principle read any position, and a gVCF also records which stretches of the genome were read confidently and which were not. That second part matters more than it sounds.
Aligned reads, the BAM or CRAM file, are the raw sequencing output before it is summarised into variants. They let a gene be re-examined base by base, which is what the read-level Deep Read panel needs.
A plain variant-only VCF lists the places you differ from the reference but does not record what was covered. It sits in between: clear about what it found, silent about what it could not see.
Coverage and callability, in plain words
Coverage, sometimes called depth, is how many times a single position was read during sequencing. A position read many times over can be called with confidence; a position read once, or not at all, cannot.
Callability is the share of a gene that could be read confidently in your particular file. Our glossary puts it plainly: callability is how much of a gene your file could be read confidently, and 'not found' is not the same as 'examined and absent'.
A gVCF carries this information directly, so the report can state what fraction of the panel was callable at a stated read depth and draw a gene-by-gene map. A genotyping chip has no such notion: it either holds your pre-chosen position or it does not. A variant-only VCF discards it, which is why those files are read more cautiously.
Why an absence is not a result
The single most useful habit in reading a genome report is to separate two very different kinds of blank. 'Examined and clear' means the position could be read and you carry the common reference letter. 'Never looked there' means the file did not cover it, so nothing can be said either way.
On a whole-genome file that carries coverage information, an absence can usually be read as the first kind: examined, and reference. The report says so directly, and it still suggests confirming anything that matters with a clinician and a validated gene test.
On a variant-only file, an absence is ambiguous by design. The report spells this out: an absence means no variant was reported, which could be the reference letter or a position your file simply did not cover. It never treats that silence as a confirmed result.
Chips have their own version of the trap. Because an array only probes the positions it was designed for, a rare variant it never tested for can never appear, and that silence is not reassurance. A large BMJ study (Weedon and colleagues, 2021) reported that SNP chips are unreliable for exactly these rare pathogenic variants, which is one reason the rare-variant clinical and carrier panels need a sequencing file rather than an array.
What this looks like on the sample report
The public sample report at /sample is built from a whole-genome file, so it shows the coverage machinery at work. Each read-level finding carries a small 'callable' band, the report states what share of the panel was callable, and a per-gene callability table lists, gene by gene, how much could be read.
It also shows how the positions with no variant reported are handled. The trait and exploratory sections say, in plain words, how many were read from your file and how many were not, and they label the rest as read as the common reference genotype, an inference, not a measurement. The sample is marked clearly as an illustration and not a real genome, so it is a safe place to learn the layout before reading your own report.
Reading your own report, the same habit applies: the file-type banner at the top says which kind of file you uploaded, and every empty section reads as 'not found in the regions examined', never as 'examined and clear'.
What Aimosti would (and wouldn't) show you
On a whole-genome file we show a panel-wide callable percentage at a stated read depth, a per-gene callability table, and a small 'callable' band on each read-level finding, so the evidence behind a call is visible. On a chip file we show a full report of everything an array genuinely calls, and say plainly that the rare-variant panels need a sequencing file. Wherever a section is empty we label it as 'not found in the regions examined' rather than as a clean result, and for positions with no variant reported we say how many were read from your file and how many were inferred as the common reference genotype.
What we won't claim
We won't read an empty section as 'examined and clear', and we won't hide which positions your file could not cover. We won't claim a genotyping chip found something only sequencing can find, and we won't turn 'no variant was reported' into 'you do not have this condition'. What a report can claim is bounded by the file, and we state that boundary rather than paper over it.
Bottom line. What a report can say is bounded by the file you uploaded. A genotyping chip, a whole-genome file, and aligned reads each let us read different things, and on every file type an absence can mean 'examined and clear' or simply 'never looked there'. We label which one it is, and we never read a blank as a clean bill of health.
Related: Coverage: what each file type unlocks. Restated from: GA4GH / hts-specs: The Variant Call Format (VCF and gVCF) specification · Weedon MN et al., BMJ 2021: Use of SNP chips to detect rare pathogenic variants.