Indexes slowing Insertions(Can't use Explain Insert to Analyse)
A file of 4 MB should not take 4 minutes to insert.I see your table have InnoDB engine.

I hope you first need to optimize basic InnoDB settings for that please have a look at Innodb Performance Optimization Basics 

Now How to speed up InnoDB Inserts

There's an entire document  dedicated to bulk loading data into InnoDB. The main points:


disable autocommit to avoid an extra log flush for each insert statement: SET autocommit=0;...sql import;COMMIT;
disable foreign and unique checks (you can't disable all indexes completely):
SET unique_checks=0;
SET foreign_key_checks=0;


Setting innodb_flush_log_at_trx_commit = 0 (or 2) may also speedup inserts. Please note, ACID rules would love that value to be at 1.