How the committee goes through the bill
Once the recommendations of the programming sub-committee have been considered and any oral evidence sessions have been held, the committee begins with the first clause of the bill. Let us suppose that the first amendment in the first group - the lead amendment in that group - is to Clause 1. That amendment is moved, and the debate on the question ‘That the amendment be made’ then includes debate on any other amendment (or new clause) that is grouped with it. At the end of the debate the question is decided, on a vote if necessary: after a short interval, the doors of the committee room are locked, the clerk rises and reads out the names of members of the committee. MPs say ‘Aye’ or ‘No’ or ‘No vote’; the clerk totals the votes and hands the list to the chair. He or she declares the result, says ‘unlock’ and moves on to the next question to be decided.
If a second group has its lead amendment to Clause 1, that group will be dealt with in the same way. But if not, the chair proposes the question ‘That Clause 1 stand part of the bill’. This gives the opportunity of a ‘stand part debate’ on the clause as a whole. If debate on a number of amendments to a clause has covered the ground, the chair can decide to put the question on clause stand part without further debate.
An important feature of this way of going through a bill - and one that often causes confusion - is that the amendments are decided not in the order in which they are grouped for debate but in the order in which they apply to the bill. This can mean

A typical selection list for a Commons public bill committee considering a bill under a programme order
Source: The House of Commons 2014

A typical selection list for the report stage of a bill in the House of Commons under a programme order
Source: The House of Commons 2014 that an amendment to a clause near the end of the bill may be debated with the first group at the first sitting; but it will be put to the vote only when the committee gets to that clause, which may be after many hours of consideration. If amendments have already been debated (unless they are in the name of the member in charge of the bill), they are often passed over in silence when they are reached. But if the opposition or a backbencher wants a vote - a separate division - and the chair agrees, a vote on a specific amendment may take place, but without further debate. Government amendments that are reached in this way are called formally whether or not a vote is expected; the minister says ‘I beg to move’ and the question on the amendment is put to the committee.
If no lead amendment is down to any clause, the committee must nevertheless agree whether or not the clause should stand part of the bill. When the committee has got to the end of the bill, any new clauses and new schedules (and any amendments to them) are decided upon (and debated, if they have not been grouped with earlier amendments).
When the committee has completed its consideration of a bill, the formal report of the bill appears in the Votes and Proceedings for that day, and the bill - if it has been amended - is reprinted for the report stage (see page 198). The process of going through the bill may have taken only a few minutes at a single sitting, or it may have taken 100 hours of often fierce debate over 20 or 30 sittings in the space of several weeks.