Table 3. Variant sequences detected in the first experiment with pilE from N. gonorrhoeae FA1090.

Assembly	Donorsequence	5′ sequenceidentity (nt)	Variantsequence (nt)	3′ sequenceidentity (nt)	RecA−frequency(×10−3)a	RecA+ frequency(×10−3)a	RecA+/RecA− ratiob
Allele 1	Reference	–	–	–	–	–	–
Allele 2	pilS3c1	23	169	39	0.062	10.4	168
Allele 3	pilS6c1	59	82	141	0.021	7.19	342
Allele 4	pilS2c4	42	87	39	0.070	6.42	92
Allele 5	pilS3c3	4	192	40	0.104	3.78	36
Allele 6	pilS3c1	39	10	234	0.027	15.1	559
Allele 7	pilS1c2	19	84	36	0.088	4.10	47
Allele 8	pilS7c1	35	125	106	0.018	2.68	149
Allele 9	pilS7c1 or	68	5	19	0.019	5.91	311
	pilS6c2	111	5	44
Allele 10	pilS6c1	57	178	59	0.038	7.50	197
Allele 11	pilS6c2	40	65	47	0.013	2.86	220
Allele 12	pilS1c1	8	71	228	0.034	5.96	175
Allele 13	pilS6c2	44	12	47	0.027	4.66	173
Allele 14	pilS2c1	3	96	141	0.023	4.19	182
Allele 15	pilS1c5	55	192	41	0.057	2.36	41
Allele 16	pilS3c3	56	137	23	0.104	3.48	34
Allele 17	pilS1c4	59	51	30	0.011	3.67	334
Allele 18	pilS1c4	5	6	18	0.075	0.92	12
Allele 19	pilS3c3	39	52	29	0.010	2.31	231
Allele 20	pilS7c1	56	71	68	0.024	1.78	74
Allele 21	pilS2c4	43	43	48	0.009	0.60	67
Allele 22	pilS7c1	68	62	35	0.015	4.76	317
Allele 23	pilS1c1	11	89	228	0.043	5.25	122
Allele 24	pilS1c5	6	13	18	0.003	0.81	270
Allele 25	mosaic	–	117	–	0.014	3.23	231
Allele 26	pilS3c3	5	38	26	0.019	3.02	159
Allele 27	pilEc2	47	4	42	0.031	1.22	39
Allele 28	pilS2c1 or	15	34	4	0.043	5.50	128
	pilS3c1	11	34	32
Allele 29	pilS1c2	36	40	55	0.011	4.97	452

^aThe average k-mer depth of the variant portion of the assembly divided by the average k-mer depth of same-sized regions immediately on either side of the variant sequence.

^bThe frequency in the presence of RecA divided by the frequency in the absence of RecA.