What is GC Content?
GC content is the percentage of a DNA or RNA sequence made up of guanine (G) and cytosine (C), as opposed to adenine (A) and thymine (T, or uracil U in RNA). A sequence that is 60% GC has 60 G or C bases in every 100.
What is a normal GC content?
There is no single normal value: GC content is a property of a species and of the region you look at. Genomes range from about 20% to over 70% GC, and a gene can sit far from its genome's average, so compare a sequence with others from the same organism or region rather than with a fixed number.
| Organism (genome average) | Approximate GC |
|---|---|
| Plasmodium falciparum (malaria parasite) | 19% |
| Saccharomyces cerevisiae (baker's yeast) | 38% |
| Human | 41% |
| Escherichia coli K-12 | 51% |
| Mycobacterium tuberculosis | 66% |
| Streptomyces coelicolor | 72% |
For a PCR primer the usual target is 40–60% GC (see primer design), and a PCR product much above 65% GC is likely to need extra optimisation.
Why it matters
A G–C pair has three hydrogen bonds and stacks more strongly with its neighbours than an A–T pair, so GC-rich DNA is harder to pull apart. That one fact has practical consequences:
Melting temperature. GC-rich DNA needs more heat to separate into single strands, which sets the annealing temperature of PCR primers. GC-rich primers need higher temperatures than AT-rich ones.
PCR and sequencing. Regions above roughly 65% GC form stable secondary structures and are notoriously hard to amplify; additives such as DMSO or betaine and a higher denaturation temperature often help. Sequencing runs also cover GC-extreme regions less evenly.
Biology. GC content varies along a genome. In many organisms genes sit in more GC-rich regions than the DNA between them, and CpG-rich islands often mark gene promoters.
GC content formula
GC% = (number of G + number of C) ÷ (number of A, C, G and T bases) × 100. For ATGCGC that is 4 ÷ 6 = 66.7%. Ambiguity codes such as N are left out of both counts, so one unknown base does not drag the percentage down.
GC along a sequence
One average can hide a lot, so the tool also plots a sliding window: the GC% of a short stretch that moves along the sequence. Peaks and valleys show GC-rich and AT-rich regions.
GC skew = (G − C) ÷ (G + C), calculated per window, measures whether one strand carries more G than C. In many bacteria the skew is positive on one half of the chromosome and negative on the other, because the leading and lagging strands are copied differently. The cumulative skew adds the values up as it goes: its minimum usually marks the replication origin and its maximum the terminus (Grigoriev 1998). AT skew is the same idea for A and T.
GC content across a genome
GC content is not spread evenly. In the human genome long stretches (called isochores) are alternately GC-richer and AT-richer, and gene-dense regions tend to be the GC-richer ones. Short GC-rich stretches called CpG islands often mark the start of genes. A sliding window shows these shifts; the whole-sequence average hides them. The "GC along a sequence" section below explains how the window works.
How Aaron's Archive does it
| Item | What the tool does |
|---|---|
| GC% | (G + C) ÷ (A + C + G + T) × 100 over the whole sequence; works for DNA and RNA. |
| Window size | 100 bp for sequences up to about 20 kb, never below 20 bp for very short ones, and length ÷ 200 above 20 kb so a plot never has more than about 400 points. The size is printed next to the chart. |
| Skew | GC skew, AT skew and cumulative GC skew on the same windows. |
Pitfalls
Skew only means something on stretches of tens of kilobases or more; on a short sequence it is mostly noise. A GC value is a description, not a verdict: unusual GC does not by itself say a region is a gene, a promoter or an error. And if you entered the opposite strand of a genome, the skew signs and the origin/terminus pattern flip.
Common questions about GC content
How do I calculate GC content by hand?
Count the G and C bases, divide by the total number of bases, and multiply by 100. For ATGCGC that is 4 ÷ 6 × 100 = 66.7%.
Is a high GC content good or bad?
Neither. It is a property of the organism and the region. It only becomes a problem in practice: very GC-rich DNA is hard to amplify by PCR and to sequence, because it holds together and folds into stable structures.
Why does GC content change melting temperature?
A G–C pair has three hydrogen bonds and an A–T pair has two, and G–C stacking is also stronger. More G and C therefore means a higher melting temperature. See melting temperature.
Is GC content the same for RNA?
Yes. Count G and C and divide by the length. RNA has U where DNA has T, which does not change the GC count.
Where can I calculate it?
Use the GC content calculator: paste a sequence and read the percentage, the base counts and the window plot.