I have been looking at IRS.gov/Where'sMyRefund? every week since May 3, when my tax return was filed.  This week I got an answer that said "You do not get a refund. Instead you owe us $3118 in Federal Income Tax. We will send you a letter about this on August 9."

Why are they taxing 100% of my total income? Even my Social Security?

I found a button labeled "Transcript" which showed me the figures TurboTax put onto the 1040 form and comparing those numbers with what the IRS would have put in.  They put $0.00 for Standard Deduction. For Schedule A, they put only $1723.00 in deductions, which they did NOT put toward my tax liability.

Why am I paying taxes on 100% of my income? Including my Social Security?

Why did they put $0.00 for Standard Deduction?

Why did they NOT allow Charitable Contributions on my Schedule A?