@Override
	public double[] computeValue(final char refBase, FastaWindow window, AlignmentColumn col) {
		value[0] = 0;
        double counted = 0;
		if (col.getDepth() > 0) {
			Iterator<MappedRead> it = col.getIterator();
			while(it.hasNext()) {
				MappedRead read = it.next();
				if (read.hasBaseAtReferencePos(col.getCurrentPosition())) {
					char b = (char)read.getBaseAtReferencePos(col.getCurrentPosition());
					if (b == 'N' || refBase == 'N') 
						continue;
					
					value[0] += read.getMismatchCount(window);
                    counted++;
				}
			}
		}
		
		if (counted > 0)
			value[0] = value[0] / counted;

		return value;
	}