Just another thought: Who on earth thought John was an Indian from Europe? According to the Emerett Nicholson Papers and the book the Sharp, Nicholson and Thompson families of East Texas, both state he was an Irish seaman. This would be in line with other data from JV Thompson, that shows the line Scot-Irish. He then traces the lineage back to Scotland Johannes Van Kirk Thomson, ca, 1400 from Dumbarton, Scotland.
The Native lines, if wny, are through his wifes Alsey Butt's line back to Jane Etheridge the wife of Thomas Etheridge, the great grandparents of Alsey Butt, making her at a maximum of 1/8 Indian. There was no Native lines in the Thompson family of this line prior to that. Hope this helps.