Here is a rough example (not 100% right but close enough and obviously I haven't seen the OPs tax form) of what is going on:
55k of income
27k of 401(k) (17.5 yours +10k of company match)
5500 ira contribution
= 23k of agi
7.7k of payroll taxes
1200 in federal taxes
1.2k/55k = 2% federal income tax rate
1.2/23k = 5% federal income tax rate
8.9k tax /23k agi = 38% effective tax rate
8.9/55k = 16% effective tax rate
AGI is not income and federal taxes are not the big tax on low income wage earners.
Unless your taxes paid over the last year was about $9,000, there's a math error. The only way I could see something like this happening is if you had a very large property tax item.