After a bill is introduced, it may be assigned to one or more committees. Prior to debate by the whole Congress, the committee may issue a report on their recommendations. Reports are assigned separate sequential numbers within each chamber (e.g., H. Rpt. 99-1, S. Rpt. 99-1).
A conference committee report is a particular type of committee report issued after passage in both chambers. Members from the House and Senate meet to resolve differences between two versions of the bill. The committee prepares a report which discusses only the provisions that differed and contains the agreed-upon language of the bill and an explanation of the compromise.
Note that the conference committee report is numbered in the same format as other committee reports so you often cannot tell the difference between a committee report and a conference committee report based on citation only.