I hope you do have the relevant qualifications to perform the duties that you are claiming in your reference letter, also Form 16s and payslips and bank statements showing salary deposits may help in allaying any concerns they may have. If they are still not convinced, they may ask for a personal interview, but I dont think that it warrants rejection at this stage. In my opinion a third-party reference letter may not be valid, it is as good as a self-attested declaration. Dont give up hope yet, many applicants between June 4 and June are still awaiting payment charge. Hope this helps. Best of luck.