Every stage has a different scrutiny parameter. Application may be rejected at any stage. However chances are much lesser after PER issuance.
In simple layman's terms,
First step is completeness check where apps are checked to see that all docs are in place.
App is charged on successful application.
First line in ECAS is updated.
Next is eligibility check where apps are checked on the basis of the 6 eligibility criteria and points calculated.
PER is issued after this if app meets CIC standards.
Next the App is transferred to the respective VO either by hard copy or electronically or both.
VO then does app scrutiny one more time, background check and security checks.
2nd line in ECAS is updated.
If applicable, applicant may be called for interview.
Then MR is issued subject to satisfactory completion of background checks.
Applicant undergoes medical tests with panel physicists.
Once positive MR results are recd by VO, 3rd line in ECAS is updated.
Security checks if any are done.
Passport request is sent to applicants.
4th Line in ECAS is updated
Applicant sends passports to VO / embassy for stamping
Passport is signed, stamped with COPR and sent back to applicant
Applicant has to complete landing formalities within 12 months of MR..