The contribution limit for your SEP-IRA contribution is generally independent of limit for your regular traditional IRA contribution (which should be made to a different IRA account to avoid any confusion about the type of contribution). Your SEP-IRA contribution reduces your eligible compensation available to contribute to a regular IRA, but it seems likely that you have sufficient compensation to cover a $6,500 IRA contribution after allocating a portion of your net earnings from self-employment to a SEP-IRA contribution.
Whether or not a traditional IRA contribution will be deductible will depend on your modified AGI and your filing status.
