The top spellings for phonemes and their percentages of the 17,000 most frequent words were investigated by Paul Hanna (see Hodges, R E. (1966). The case for teaching sound-to-letter correspondences in spelling. Elementary School Journal, 66, 327-336, and the update, Fry, E. (2004). Phonics: A large phoneme-grapheme frequency count revisited.  Journal of Literacy Research, 36, 85-98).  I will only include graphemes that account for at least 3% of the example words. For the reliability of phonics generalizations, see the chart below summarizing Francine Johnston's research.

Phoneme	Principal spellings in order of frequency (Hanna, Fry) and example words
/a/	a (sack), 97%; a_e (have), 3%
/A/	a (bacon), 45%; a_e (bake), 35%; ai (raid), 9%; ay (play), 6%
/Ar/	ar (parable), 29%; are (bare), 23%; air (fair), 21%; ere (there), 15%; ear (bear), 6%
/ar/	ar (bar), 89%; are (are), 5%; ear (heart), 3%
/aw/	o (lost), 41%; a (ball), 22%; au (haul), 19%; aw (saw) 10%
/b/	b (big), 97%
/ch/	ch (chair), 55%, t (feature), 31%; tch (catch), 11%
/d/	d (do), 98%
/u/ (schwa)	o (other), 24%; u (up), 20%; a (alarm), 19%; i (panic), 18%; e (enough), 11%; ou (famous), 5%
/e/	e (bed), 91%; ea (bread) 4%
/E/	y (very), 41%; e (beware), 40%;  ee (feet), 6%; ea (seat), 6%
/Er/	er (experience), 32%; ear (fear), 25%; eer (deer), 18%; e_e (here), 14%; ier (tier), 7%
/ul/	le (table), 95%
/er/	er (hammer), 77%; or (odor), 12%; ar (cellar), 8%
/f/	f (fox), 78%; ph (phone), 12%; ff (stuff), 9%
/g/	g (girl), 88%; gg (egg), 5%; x (exit), 3%
/h/	h (hot), 98%
/hw/	wh (white), 100%
/i/	i (hit), 92%; i-e (give), 6% [y (gym), 2%]
/I/	i_e (pipe), 37%; i (Bible), 37%; y (by), 14%; igh (right), 6%
/j/	ge (age), 66%; j (jet), 22%; dge (edge), 5%; d (soldier), 3%
/k/	c (car), 73%; k (kit), 13%; ck (sick), 6%; ch (choir), 3%
/ks/	x (six), 90%; cs (tocsin), 10%
/kw/	qu (quit), 97%
/l/	l (leg), 91%; ll (tell), 9%
/m/	m (mad), 94%; mm (dimmer), 4%
/n/	n (no), 97% [kn (know)<1%]
/ng/	ng (sing), 59%; n (monkey), 41%
/o/	o (hot), 94%; a (want), 5%
/O/	o (focus), 73%; o_e (hope), 14%; oa (boat), 5%; ow (row), 5%
/oi/	oi (oil), 62%; oy (toy), 32%
/oo/	u (bush), 61%; oo (hook), 35%; o (woman), 5%
/Or/	or (for), 97%; ore (core), 3%
/ow/	ou (shout), 56%; ow (howl), 29%; ou_e (house), 13%
/p/	p (pin), 96%, pp (happen), 4%
/r/	r (run), 97%
/s/	s (say), 73%, c (cereal), 17%; ss (toss), 7%
/sh/	ti (action), 53%; sh (shy), 26%; ci (special), 5%; ssi (fission), 3%
/t/	t (top), 97%
/th/	th (bath) 100%
/u/	u (bus) 86%; o (ton), 8%
/U/ or /OO/	u (human), 59%; u_e (use), 19%; oo (moon), 11%; ew (few) 4%
/v/	v (very), 99.5%
/w/	w (way), 92%; u (suede), 7.5%
/y/	i (onion), 55%; y (yes), 44%
/z/	s (was), 64%; z (zero), 23%; es (flies), 4%, x (xylophone), 4%
/zh/	si (incision), 49%; s (pleasure), 33%; g (garage), 15%

The frequency of spelling patterns is a matter of scientific discovery.  Much of what I learned from Hanna's study surprised me, e.g., that s is the most common spelling of /z/.  We don't want to burden children and teachers with rare spellings, nor do we want to omit common ones.

See also my list of phonemes, common spellings, and meaningful names.
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