Table 2.

Sequencing filtering and clustering statistics.

	Total reads	Joined reads passing filtering	% Reads passing filtering	Singletons	% Singletons	TCRβ sequence clonotypes	Clonotypes >0.0001 read frequency
Pt 1 day 0	712,114	578,962	81.30	138,579	23.94	96,342	351
Pt 1 day 14	634,288	509,817	80.38	123,369	24.20	86,115	309
Pt 1 day 28	678,888	541,744	79.80	131,904	24.35	91,304	273
Pt 1 day 84	729,463	587,775	80.58	129,391	22.01	94,690	351
Pt 2 day 0	757,735	605,308	79.88	59,620	9.85	53,696	649
Pt 2 day 14	780,672	634,618	81.29	53,667	8.46	45,556	735
Pt 2 day 28	719,236	582,503	80.99	48,491	8.32	37,518	889
Pt 2 day 84	794,255	619,977	78.06	48,074	7.75	35,749	1,056
Pt 3 day 0	730,970	568,087	77.72	142,900	25.15	102,441	202
Pt 3 day 14	742,921	603,994	81.30	62,924	10.42	57,993	380
Pt 3 day 28	715,794	591,947	82.70	161,392	27.26	109,160	168
Pt 3 day 84	679,172	535,881	78.90	162,876	30.39	98,310	168
Pt 4 day 0	805,599	636,395	79.00	112,244	17.64	71,884	729
Pt 4 day 14	705,899	568,716	80.57	50,552	8.89	41,283	820
Pt 4 day 28	434,032	346,336	79.80	79,450	22.94	47,085	590
Pt 4 day 84	677,674	528,767	78.03	81,657	15.44	67,809	661
Pt 5 day 0	706,399	572,666	81.07	174,381	30.45	94,164	335
Pt 5 day 14	751,609	606,642	80.71	119,104	19.63	94,296	315
Pt 5 day 28	806,787	641,859	79.56	111,678	17.40	97,188	288
Pt 5 day 84	692,772	545,476	78.74	129,638	23.77	91,356	274
Pt 6 day 0	853,716	660,961	77.42	201,954	30.55	111,499	269
Pt 6 day 14	838,230	666,127	79.47	146,402	21.98	111,654	246
Pt 6 day 28	764,235	630,828	82.54	148,399	23.52	113,641	210
Pt 6 day 84	840,148	677,297	80.62	103,453	15.27	100,277	228