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I know some elementary chemistry and biology. I also think I know what a gene is (it's a sequence of DNA which encodes a particular protein). I also know that on a chromosome there are sections of DNA which are kind of junk and do nothing. But being armed with this information, doesn't seem enough for me to understand what it means to "map the human genome".

Some possibilities:

  1. a. It tells me the entire sequences of nucleotides that make up a particular human's chromosomes (it could not possibly do this for humans in general because of course the sequence is different from one human to another).

    b. It tells me the entire sequences of nucleotides that make up a human's chromosomes... with some annotations along the lines of "at this point in the molecule, we could optionally have nucleotides A, B or C".

  2. It tells me the start and stop points for each of the genes along the chromosome.

  3. It tells me the function of every gene.

  4. Something completely different!

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  • $\begingroup$ Suggested edit changing molecules/atoms to nucleotides for accuracy/clarity, DNA is composed of nucleotides, a very specific subset of molecules which are composed of atoms. Molecules are composed of bonded atoms, atomic structure is not of particular interest, but would be inferred from the nucleotide sequence (and could vary for a given Dna sequence depending on pH and DNA modifications). $\endgroup$
    – InactionPotential
    Commented Jun 22, 2015 at 16:16
  • $\begingroup$ "Mapping" the genome is ambiguous. Originally it meant making a genetic map, which involved finding the ordering of various genetic markers but not the sequence of nucleotides. Mostly these days people are interested in a genome sequence which is seldom described as "mapping" by researchers. $\endgroup$
    – Michael Hoffman
    Commented Jun 22, 2015 at 17:33

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So, the very first map of the human genome was of a few pooled samples with a single nucleotide called at each position.

This is basically okay, though, because humans are 99.9 (with possibly a few more 9s) % similar to one another. So you can get a lot of broadly-applicable information out of a single individual's DNA.

Further genome-mapping efforts brought data from new individuals and started to give us information about variants, like in your option 1b. At this point, there are projects like the 1000 Genomes Project that are trying to get 1000 full human genomes from a variety of ethnic groups sequenced and to characterize all the common variations.

Your point 2 was a different project, but was also part of mapping the genome. It's mostly complete now-- in that we know almost all of the RNA sequences that are produced by most cell types and mostly where they come from on the genome, with a few mysteries left around the edges.

Point 3-- no. Lots about the genome we still don't know. We're pretty good about where genes are encoded, but how they're regulated, how they interact... and remember that the part of the genome that codes for genes is a very small percentage of the overall sequence. Something like the the ENCODE Project is trying to figure out the various biochemical interactions present at every position of DNA, but even if that data were complete and reliable, which it's not, it still wouldn't tell us the "purpose" of all DNA.

So, when we say we've "mapped" a genome, we generally mean (A) we have (something pretty close to) full sequence of at least one individual's DNA (or a consensus sequence from a pool) and (B) we know where genes are on it. That's a huge step but only the beginning of understanding genetics. In the case of humans, we're adding on to that understanding by learning where variants are and how common they are.

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    $\begingroup$ As this answer suggests, mapping the location of known genes to their location in the genomic sequence is a specific (but important) example of genome mapping. More generally, mapping is identifying the location or locations of a sequence or sequences of interest in the genome. This can be genes, transcription factor binding sites, mapping variations in sequences associated with different human populations or with certain diseases, etc. $\endgroup$
    – InactionPotential
    Commented Jun 22, 2015 at 16:30
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    $\begingroup$ The sequence from the International Human Genome Sequencing Consortium was actually a mosaic of DNA different donors, not one individual. $\endgroup$
    – Michael Hoffman
    Commented Jun 22, 2015 at 17:32
  • $\begingroup$ Good point, I'll edit. I was thinking of the Celera DNA, which I thought was Venter's, but it turns out that they were using a pool, too. (Venter was just in the pool.) $\endgroup$
    – Transcriptase
    Commented Jun 22, 2015 at 18:16
  • $\begingroup$ The Celera genome is indeed mostly from Craig Venter, but this is not true for the HUGO project and today there is more data in it anyways. $\endgroup$
    – Chris ♦
    Commented Jun 22, 2015 at 18:20
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    $\begingroup$ InactionPotential raises a very important point. Mapping does not necessarily involve sequencing. There were maps of the human genome long before it was sequenced. There were also maps of other organisms long before sequencing was even invented. Like geographic mapping, genome mapping establishes spatial relationships between "interesting" loci. $\endgroup$
    – canadianer
    Commented Jun 22, 2015 at 21:04

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