construct a sql , assign it to a variable and execute inside shell script

I am trying to execute a mysql query inside my shell script, which is not executing . Here is what i am trying to do

query="\"select count(*) from information_schema.tables where TABLE_SCHEMA not in ('mysql','performance_schema','information_schema') and engine!='INNODB';\"" 

echo $ query

"select count(*) from information_schema.tables where TABLE_SCHEMA not in ('mysql','performance_schema','information_schema') and engine!='INNODB';" 

Inside my shell script , i am executing below which is not working. It is not giving any error but simply not considering -e option and listing down all the valid options for mysql client.

mysql -u$  username -p$  password -e$  query 

I even validated below in my shell prompt

echo "mysql -uroot -p -e$  query" mysql -uroot -p -e"select count(*) from information_schema.tables where TABLE_SCHEMA not in ('mysql','performance_schema','information_schema') and engine!='INNODB';" 

which is perfectly fine and executes without any issues. I am not sure what to do now. please help.Thanks