Javascript FileReader reads file incorrectly

I have a short JavaScript function which will take an uploaded file and display the hex equivalent of it. Comparing the original file and the output in a hex-editor shows that they are partially different but not completely.

String.prototype.hexEncode = function(){
  var hex, i;

  var result = "";
  for (i = 0; i < this.length; i++) {
    hex = this.charCodeAt(i).toString(16);
    result += ("" + hex).slice(-4);
  }

  return result
}

function upload() {
  var file = document.getElementById("fileToUpload").files[0];
  var reader = new FileReader();
  reader.readAsText(file, "windows-1252");
  reader.onload = function (evt) {
    var program = evt.target.result.hexEncode();
    program = program;
    console.log(program);
  }
}

Here are the original file and the output next to each other:

2A 2A 54 49 38 33 46 2A 1A 0A 0A 43 72 65 61 74
2A 2A 54 49 38 33 46 2A 1A AA 43 72 65 61 74 65

What is causing the difference in outputs? Any help would be greatly appreciated.

To generate an Hex dump in js, you won't want to use the readAsText method, which will convert your data in either UCS-2 or UTF-16, instead, read directly the binary data you'll get from the readAsArrayBuffer method, and work from there:

function hexDump(file) {
  return new Promise((res, rej) => {
    if (!(file instanceof Blob)) rej('wrong input');
    const reader = new FileReader();
    reader.onload = e => {
      res(hex(reader.result));
    };
    reader.onerror = e => rej('error while reading');
    reader.readAsArrayBuffer(file);
  });
  // gotten from https://developer.mozilla.org/en-US/docs/Web/API/SubtleCrypto/digest#Example
  function hex(buffer) {
    const hexCodes = [];
    const view = new DataView(buffer);
    for (let i = 0; i < view.byteLength; i += 4) {
      // Using getUint32 reduces the number of iterations needed (we process 4 bytes each time)
      let value = view.getUint32(i)
      // toString(16) will give the hex representation of the number without padding
      let stringValue = value.toString(16)
      // We use concatenation and slice for padding
      let padding = '00000000'
      let paddedValue = (padding + stringValue).slice(-padding.length).toUpperCase();
      hexCodes.push( // simple prettyfying
        paddedValue.slice(0,2),
        paddedValue.slice(2,4),
        paddedValue.slice(4,6),
        paddedValue.slice(6,8)
        );
    }
    return hexCodes.join(' ');
  }
}

// How to use it
inp.onchange = e => hexDump(inp.files[0].slice(0, 100)) // for demo I slice the file
    .then(hex => console.log(hex))
    .catch(e => console.error(e));