Conflicts faced While Load Testing

I was working on load testing of a web application last month, results were very conflicting when I was accessing application from browser response was very good but while executing script from Jmeter throughput was very less.

I had applied all possible optimizations like :
1. Query Caching
2. Output compression (mod_deflate)
3. Minify JS and CSS

but result was same.
I enabled logs to see compression ratio and realized that Jmeter was not sending accept-encoding HTTP header so Apache was not sending compressed result and that was affecting throughput.
After adding accept-encoding header throughput was as desired.