Table 2. The n=24 positions with a significant association with cefotaxime resistance (FDR ≤0.05) and a Consistency Index ≤ 0.05882353. Homoplasy-based association analysis pyseer Genomic position mutation Counts ACGT Min changes CI crosstab AF pvalue Fisher FDR Gene name Genomic position mutation AF filterpvalue lrtpvalue 810581 A>G 41:0:122:0 18 0.056 0:22:26:34 6.83E-01 8.11E-05 0.039 glcE 810581 A>G 0.683 1.87E-04 2.09E-02 810791 G>T 0:0:54:109 17 0.059 0:22:28:32 6.59E-01 1.68E-05 0.035 glcE 810791* GGGT>TGGC 0.646 4.08E-04 1.94E-02 815680 C>T 0:69:0:93 18 0.056 2:20:34:26 5.61E-01 1.06E-04 0.042 glcA 815680 C>T 0.561 1.20E-04 2.07E-02 824522 T>C 0:82:0:73 18 0.056 2:20:36:24 5.37E-01 3.58E-05 0.036 gspC 824522* T>C 0.378 8.08E-06 1.00E+00 828695 A>G 79:0:74:0 18 0.056 3:19:41:19 4.63E-01 1.14E-05 0.034 gspF 828695 A>G 0.463 1.08E-05 3.26E-02 830684 T>C 0:80:0:73 18 0.056 2:20:37:23 5.24E-01 1.61E-05 0.034 gspI 830684* T>C 0.488 3.74E-05 1.06E-01 830708 A>G 68:0:85:0 19 0.053 2:20:36:24 5.37E-01 3.58E-05 0.036 gspI 830708* A>G 0.11 6.41E-01 5.02E-01 830732 T>C 0:82:0:71 17 0.059 2:20:36:24 5.37E-01 3.58E-05 0.036 gspI 830732 T>C 0.537 4.20E-05 4.19E-02 831564 G>A 71:0:83:0 17 0.059 5:17:45:15 3.90E-01 2.76E-05 0.036 gspK 831564 G>A 0.39 1.71E-05 2.37E-01 832152 T>C 0:86:0:72 18 0.056 2:20:28:22 5.83E-01 1.08E-05 0.034 gspK 832152* CGTCG>TGTCA 0.195 6.94E-03 2.29E-01 832287 A>T 81:0:0:79 17 0.059 2:20:37:23 5.24E-01 1.61E-05 0.034 gspK 832287* T>A 0.232 6.73E-02 5.73E-01 833451 A>T 64:0:0:98 20 0.05 1:21:34:26 5.73E-01 1.03E-05 0.034 gspL 833451* T>A 0.378 1.69E-04 9.04E-02 843887 G>A 64:0:40:0 19 0.053 21:1:29:31 3.90E-01 7.00E-05 0.036 unnamed 843884* GTTGCGC>TCGACGT 0.354 4.08E-04 1.08E-01 1863004 A>G 126:0:46:0 18 0.056 9:13:53:7 2.44E-01 3.37E-05 0.036 thiM 1862989* CTGTCTCATAAGCCAACCGCC > TTATCTTTTAAACCGGCAGCG 0.232 4.55E-05 3.30E-02 1911551 T>C 0:116:0:44 17 0.059 16:6:14:46 6.34E-01 7.02E-05 0.036 unnamed 1911551* C>T* 0.28 1.22E-03 5.28E-01
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