Table 3.

Accuracy (ACC) and positive prediction rate (PPR) of identifying SHMs in the complementarity determining region 3 (CDR3) from the simulated clonally expanded BCRs.

	Lineage generation	# of SHMs in 125-bp BCR sequence	TP	TN	FP	FN	ACC	PPR
BRILIA human	Germline	0	0	51,544	1,031	0	0.98	0.00
	1st	5	1,230	50,072	629	644	0.98	0.66
	2nd	10	2,433	48,146	676	1,320	0.96	0.78
	3rd	15	3,373	46,141	755	2,306	0.94	0.82
	4th	20	4,376	44,310	633	3,256	0.93	0.87
	5th	25	5,588	42,370	612	4,005	0.91	0.90
VQUEST + JA human	Germline	0	0	46,724	502	0	0.99	0.00
	1st	5	913	44,296	812	758	0.97	0.53
	2nd	10	1,636	41,973	844	1,645	0.95	0.66
	3rd	15	2,146	39,634	919	2,745	0.92	0.70
	4th	20	2,365	36,937	1,010	4,007	0.89	0.70
	5th	25	2,324	33,983	1,114	5,410	0.85	0.68
partis human	Germline	0	0	50,685	654	0	0.99	0.00
	1st	5	1,160	48,182	1,149	665	0.96	0.50
	2nd	10	2,325	45,946	1,695	1,334	0.94	0.58
	3rd	15	3,505	43,251	2,228	2,001	0.92	0.61
	4th	20	4,655	40,405	2,828	2,686	0.89	0.62
	5th	25	5,648	37,713	3,154	3,441	0.87	0.64
BRILIA mouse	Germline	0	0	42,144	804	0	0.98	0.00
	1st	5	976	41,062	410	500	0.98	0.70
	2nd	10	1,976	39,518	443	1,011	0.97	0.82
	3rd	15	2,746	37,891	527	1,784	0.95	0.84
	4th	20	3,531	36,427	421	2,569	0.93	0.89
	5th	25	4,579	34,951	374	3,044	0.92	0.92
VQUEST + JA mouse	Germline	0	0	38,602	209	0	0.99	0.00
	1st	5	743	36,843	459	592	0.97	0.62
	2nd	10	1,407	35,471	522	1,315	0.95	0.73
	3rd	15	1,864	33,978	639	2,270	0.92	0.74
	4th	20	2,176	32,294	680	3,328	0.90	0.76
	5th	25	2,298	30,090	739	4,346	0.86	0.76

Accuracy is computed as (TP + TN)/(TP + TN + FN + FP), where T = true, P = positive, F = false, and N = negative. PPR is computed as TP/(TP + FP). The nucleotides in the CDR3 are pooled together based on the sequence lineage (e.g., 1st descendants of the Germline B cells), prior to determining the SHM accuracy statistics. The total nucleotide count differs among algorithms because the annotation coverage differs.