Step 1 of 3

What Is a Reference Sequence?

A reference sequence is a "map" genome that scientists agree to use as a common standard, much like a well-known city map everyone navigates by. It's a long string of DNA bases (A, T, G, C) representing a typical version of an organism's genome. When researchers sequence a new sample, they compare it against this reference to spot differences or confirm matches. It won't perfectly match any one individual, but it gives everyone a shared set of coordinates to work from. In this game, our toy genome plays the role of a reference sequence.

Step 2 of 3

What Is a Read?

A sequencing machine can't read an entire genome in one pass, so it chops the DNA into millions of short fragments and reads each one separately. Each of these short fragments is called a "read," often just tens to hundreds of bases long. Reads are like puzzle pieces: alone they don't tell you much, but together they can reconstruct or be compared against a full genome. In this game, the short snippet you're given is a read pulled from somewhere in the reference genome, and your job is to figure out where it belongs.

Step 3 of 3

What Is an Aligner?

An aligner is a program that takes reads and figures out where each one best matches within a reference sequence, like a search tool scanning for the exact spot a short snippet came from. This step, called "alignment," is one of the very first things done in most genomics analyses, since you need to know where a read came from before you can study mutations or gene activity. Real aligners handle millions of reads at once and tolerate small mismatches, but the core idea is the same one you're about to try. In the next steps, you'll play the role of an aligner!

The Toy Genome

Here's our 30bp reference genome. Take a look before you start aligning reads to it.

A Adenine T Thymine G Guanine C Cytosine

Align the Read

Read 1 of 5

Score: 0

Sample Complete!

Before Sample 3

What Is Coverage?

Coverage is how many different reads overlap a given position in the genome. If ten separate reads all happen to include base #50, that base has "10x coverage." Higher coverage gives scientists more confidence in what's really there, since a random error in one read gets outvoted by all the others that agree. Very low or zero coverage means we simply don't have data for that spot — sometimes by chance, but sometimes because that piece of DNA is genuinely missing from the sample. In the next sample, pay close attention to how your reads pile up across the genome.