In the /apache-jmeter-2.13/bin folder, the jmeter.properties files states as follows:
#---------------------------------------------------------------------------
# Aggregate Report and Aggregate Graph - configuration
#---------------------------------------------------------------------------
#
# Percentiles to display in reports
# Can be float value between 0 and 100
# First percentile to display, defaults to 90%
# aggregate_rpt_pct1=90
# Second percentile to display, defaults to 95%
# aggregate_rpt_pct2=95
# Second percentile to display, defaults to 99%
# aggregate_rpt_pct3=99
Copy this to user.properties file and uncomment the aggregate_rpt_pct1=90to get 90th percentile in the generated Aggregate Report.
You can add e.g aggregate_rpt_pct3=70 to get the 70th percentile in the generated Aggregate Report.