The - s in the Present Simple

As you know, we add an -s in the Present Simple when we talk about he, she or it.

He reads

She cooks

It explains

But you have probably realized we sometimes add -es, or change a y into ie when adding -s.

These are the spelling rules:
(The chart is copied from http://www.learnenglishlanguagewell.com/grammar/verbs-with-s-in-present-simple/)
 

Spelling of third person singular forms in Present Simple Tense
Most verbs: Add “s” to infinitive(1) verbs finishing with  one vowel + “y” :add “s”	Work ->	works	Sit ->	sits
	Stay ->	stays (1)	See ->	sees
	know ->	knows	Live ->	lives
*Verbs ending with consonant and “y”: Change “y” for “ies”	Cry->	cries*	Hurry->	hurries*
	Fly->	flies*	Imply->	implies*
	Try->	tries*
Verbs ending in sibilant sounds –s, -z, -ch, -sh, or -x add “es” to infinitive	Push->	pushes	Fix->	Fixes
	Catch->	catches	Confess->	confesses
	Buzz->	buzzes	Finish->	finishes
Verbs ending with “o” Verb “have”	Go->	goes	Do->	does
	Have->	has