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 |
The 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.
The frequency in the presence of RecA divided by the frequency in the absence of RecA.