Just what Utsa has said in all likely hood

If you are electrophoresing intact mammalian genomic DNA, you have a series of problems. First, the smallest human chromosome is too large to even enter, intact, the gel using Pulsed-Field Gel Electrophoresis (PFGE). Ideally you should be using the Transverse Alternating Field Electrophoresis (TAFE) version of PFGE.

Second, the native chromosome (even as naked DNA) is a series of large (2 Mbp) loops that will be pulled into the gel part way, until parts of the loops get caught in the gel plug in which the cells were lysed and deproteinized). That's probably the faint band near the top of the gel (connecting the plug to the upper part of the gel lane.

Third, to even see such large DNAs, you should be using markers in the Mbp range, not kbp. If the cells were irradiated before lysis, generating DNA fragments, these would be what you would see running into the gel as bands of DNA smaller than the S. pombe chromosomes as markers. The gel runs would be in the 10 - 20 hours range.

Fourth, if the DNA was randomly fragmented by your procedures, you would be able to analyse the gel by using the "Broken stick model" or the Q-function (look up Bjorn Cederwal's publications) and determine the fragment-size distribution profile which fits your observed data and from this determine the number of Double-Strand Beaks (DSBs) induced per Mbp as a function of treatment dose and the original control fragment sizes. N.B. For this you would also need a denser layer of agarose at the bottom of your gel to be able to capture all fragment sizes to calculate fraction of the DNA smaller than each marker band (S. pombe and S. cerevisiae chromosomes).

Fifth, you should have probably treated your sample plugs with RNAse and Proteinase K to remove any RNA and protein in your sample and used Syber Green II to visualize the DS DNA.

It's usually the 'impurities' that gather at the bottom of the gel. If you incorporate a proteinase K and an RNAse step you should be able to significantly reduce these.