If I understand your question correctly:

For the x-axis ticks, I would use D3's axis.tickformat function. You could create a function mapXToRunNumber(x) that takes an x value and returns a run number (you seem to be close to having this already). Then, you would use: chart.xAxis.tickFormat(mapXtoRunNumber);

For the tooltip to also show the same value as the x-axis, you would use the nvD3 function chart.interactiveLayer.tooltip.headerFormatter(mapXToRunNumber).

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