Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,026,6550CT29.5% 82.1 / 49.0 61E87K (GAA→AAA) vraRResponse regulator protein VraR
Reads supporting (aligned to +/- strand):  ref base C (16/27);  new base T (2/16);  total (18/43)
Fisher's exact test for biased strand distribution p-value = 6.38e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.11e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCA  >  USA300TCH1516_ALE/2026520‑2026791
                                                                                                                                       |                                                                                                                                        
cTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATaa                                                                                                                                     >  1:943679/1‑141 (MQ=255)
    aaCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACt                                                                                                                                 <  2:309140/141‑1 (MQ=255)
     aCTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTa                                                                                                                                <  1:72294/141‑1 (MQ=255)
       ttCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGt                                                                                                                              <  1:300502/141‑1 (MQ=255)
        tCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCTATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGtt                                                                                                                             <  2:88646/141‑1 (MQ=255)
         ccGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTa                                                                                                                            <  1:863576/141‑1 (MQ=255)
         ccGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTa                                                                                                                            >  2:175550/1‑141 (MQ=255)
           ggTTAAAAAACAGATTCTCCTCTAGTAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAAc                                                                                                                          <  2:12247/141‑1 (MQ=255)
                   aaCAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATAc                                                                                                                  >  1:479220/1‑141 (MQ=255)
                      aGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACttt                                                                                                               >  1:524532/1‑141 (MQ=255)
                      aGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATATAACAATCGAAAAAAGCCCCTAATAAATGTTCTTAATCTTATACTTCAATAAAATTAGTTAACATTAATACatt                                                                                                               >  1:584368/1‑141 (MQ=255)
                       gATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTa                                                                                                              <  1:251154/141‑1 (MQ=255)
                       gATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTGTa                                                                                                              >  2:253475/1‑141 (MQ=255)
                        aTTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTaa                                                                                                             >  1:955679/1‑141 (MQ=255)
                         ttCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAAt                                                                                                            <  1:49701/141‑1 (MQ=255)
                          tctcCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAAtt                                                                                                           >  1:666843/1‑141 (MQ=255)
                           ctcctcTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAAttt                                                                                                          >  2:235469/1‑141 (MQ=255)
                               tctAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCgg                                                                                                      <  1:570765/141‑1 (MQ=255)
                                ctAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGt                                                                                                     <  1:448150/141‑1 (MQ=255)
                                ctAGAAGTTTTACGAACTGCATCGGCGATATCATTTGCACTCGTTGTTTTTAAAATGTAACTATCGACACATGACTCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGt                                                                                                     <  1:492184/141‑1 (MQ=255)
                                 tAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTa                                                                                                    <  1:508279/141‑1 (MQ=255)
                                   gAAGTTTTACGAACTGCATCGCCGATTTCGTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTaaa                                                                                                  >  2:200898/1‑141 (MQ=255)
                                    aaGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGNTAACATTAATACNTTAATTTGCGGTAAAt                                                                                                 <  1:556975/141‑1 (MQ=255)
                                     aGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATc                                                                                                <  2:73408/141‑1 (MQ=255)
                                       ttttACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtt                                                                                              <  1:79702/141‑1 (MQ=255)
                                         ttACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtttt                                                                                            <  2:308991/141‑1 (MQ=255)
                                         ttACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtttt                                                                                            >  1:846635/1‑141 (MQ=255)
                                         ttACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtttt                                                                                            >  1:271497/1‑141 (MQ=255)
                                          tACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCttttt                                                                                           >  1:217110/1‑141 (MQ=255)
                                            cGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTa                                                                                         >  2:131690/1‑141 (MQ=255)
                                               aCTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATc                                                                                      <  1:617306/141‑1 (MQ=255)
                                                cTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCt                                                                                     <  2:5705/141‑1 (MQ=255)
                                                cTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCt                                                                                     <  2:5688/141‑1 (MQ=255)
                                                   cATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAg                                                                                  <  1:158029/141‑1 (MQ=255)
                                                      cGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgtcg                                                                               <  1:800742/141‑1 (MQ=255)
                                                             atCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTc                                                                        >  1:980133/1‑141 (MQ=255)
                                                             atCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTc                                                                        <  1:194278/141‑1 (MQ=255)
                                                                 tttGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTaca                                                                    <  1:400141/141‑1 (MQ=255)
                                                                       cTTGTTGTTTTTAAAATGTAACTATCGACACCTGCAACTAAAGTACGAGATACCTCTTTATCTGCAATAAAACTAGTTAACATTAATACTTGAATTTTCGGTAAATCTTTTTTAATCTGAGTCGGCGCTTCTACAccatcc                                                              <  1:142847/141‑1 (MQ=255)
                                                                           ttgttTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGt                                                          <  1:14025/141‑1 (MQ=255)
                                                                            tgttTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTc                                                         >  1:703204/1‑141 (MQ=255)
                                                                                tttAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATcc                                                     <  1:310682/141‑1 (MQ=255)
                                                                                  tAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCAt                                                   <  1:251049/141‑1 (MQ=255)
                                                                                    aaaTGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATaa                                                 <  1:562403/141‑1 (MQ=255)
                                                                                      aTGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGt                                               <  2:164387/141‑1 (MQ=255)
                                                                                      aTGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGt                                               <  1:633522/141‑1 (MQ=255)
                                                                                               tCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCatt                                      <  1:462697/141‑1 (MQ=255)
                                                                                                          aTCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATc                           <  1:792879/141‑1 (MQ=255)
                                                                                                          aTCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATc                           <  1:354768/141‑1 (MQ=255)
                                                                                                               aTGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCt                      >  1:16405/1‑141 (MQ=255)
                                                                                                                tGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCtt                     <  1:611625/141‑1 (MQ=255)
                                                                                                                 gCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTc                    <  1:721818/141‑1 (MQ=255)
                                                                                                                      atatACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTc               <  2:329908/141‑1 (MQ=255)
                                                                                                                      atatACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTc               <  2:225524/141‑1 (MQ=255)
                                                                                                                       tataCCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCa              <  2:319467/141‑1 (MQ=255)
                                                                                                                       tataCCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCa              <  2:389161/141‑1 (MQ=255)
                                                                                                                        ataCCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCAt             <  2:138524/141‑1 (MQ=255)
                                                                                                                           ccTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGCAAATCCATTAAAATTAAATCTGGCTTCAACTCATggg          <  1:713210/141‑1 (MQ=255)
                                                                                                                             tctttatctttaATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCt        <  1:819839/141‑1 (MQ=255)
                                                                                                                                 tATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTgg    <  1:416524/141‑1 (MQ=255)
                                                                                                                                  aTCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCTGTAAATCTTTTTTAAGCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGc   <  1:736984/141‑1 (MQ=255)
                                                                                                                                   tCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCa  >  1:724236/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                        
CTAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTTGGCA  >  USA300TCH1516_ALE/2026520‑2026791

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑