Table 2. We inferred the associations between genome-wide variation and many different TCR repertoire features for productive and non-productive TCR sequences, separately.

For each TCR repertoire feature, we considered the significance of associations using a Bonferroni-corrected threshold established to correct for each TCR feature subtype, the two TCR productivity types, and the total number of SNPs tested (described in detail in Methods).

Repertoire feature(significance threshold)	Model type	Feature subtype	Productivity	Significant association
V(D)J gene usage(5.09 × 10−11)	simple	Each of 60 V-genes	Productive	Yes, for 36 V-genes
			Non-productive	Yes, for 26 V-genes
		Each of 2 D-genes	Productive	Yes, for both D-genes
			Non-productive	Yes, for both D-genes
		Each of 14 J-genes	Productive	Yes, for 7 J-genes
			Non-productive	Yes, for 8 J-genes
Amount of nucleotide trimming(9.68 × 10−10)	gene-conditioned	V-gene trimming	Productive	Yes
			Non-productive	Yes
		5’ end D-gene trimming	Productive	No
			Non-productive	No
		3’ end D-gene trimming	Productive	No
			Non-productive	No
		J-gene trimming	Productive	Yes
			Non-productive	Yes
Number of N-insertions(1.94 × 10−9)	simple	V-D-gene N-insertions	Productive	No
			Non-productive	Yes
		D-J-gene N-insertions	Productive	No
			Non-productive	Yes