Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,685,891 A→T 9.7% E184V (GAA→GTA)  clpL → ATP‑dependent Clp protease ATP‑binding subunit ClpL

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,685,8910AT 9.7% 110.9 / 3.4 52E184V (GAA→GTA) clpLATP‑dependent Clp protease ATP‑binding subunit ClpL
Reads supporting (aligned to +/- strand):  ref base A (24/21);  new base T (2/3);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 6.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

GCACAGGCAATCGTTGAAGGAAATGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGATATTTTGAAACCTGCATTAAGTCGTGG  >  USA300TCH1516_ALE/2685758‑2686023
                                                                                                                                     |                                                                                                                                     
gCACAGGCAATCGTTGAAGGAAATGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGa                                                                                                                                       >  2:329349/1‑134 (MQ=255)
 cacaGGCAATCGTTGAAGGAAATGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTAGTACTTATGAAGAAAATATTCAAAAATTAATCGaa                                                                                                                                      >  1:440547/1‑134 (MQ=255)
  acaGGCAATCGTTGAAGGAAATGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTCGAAGAAAATATTCAAAAATTAATCGAAg                                                                                                                                     <  1:260055/134‑1 (MQ=255)
      gCAATCGTTGAAGGAAATGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAATgtgt                                                                                                                                 <  2:371290/134‑1 (MQ=255)
               gAAGGAAATGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGACGGTGTTAAATC‑TTc                                                                                                                       >  2:459834/1‑134 (MQ=255)
                aaGGAAATGTACCAGTAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGATGTAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTca                                                                                                                      <  1:494279/134‑1 (MQ=255)
                     aaTGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGTAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACaaaa                                                                                                                 >  2:533159/1‑134 (MQ=255)
                      aTGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAAt                                                                                                                >  2:407000/1‑134 (MQ=255)
                      aTGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTGTTGAAGAAAATATTCAAAAATTAATCGAAGGAGTTAAATC‑TTCACAAAAt                                                                                                                >  1:381912/1‑134 (MQ=255)
                           ccAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGt                                                                                                           >  1:600978/1‑134 (MQ=255)
                           ccAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTAACAAAATGTCGt                                                                                                           >  1:263083/1‑134 (MQ=255)
                            cagcagCAATTAAATACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTa                                                                                                          <  1:526318/134‑1 (MQ=255)
                             agcagcAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCTAAAATTAATCTTAGGTGTTAAATC‑TTCACAAAATGCCGTAc                                                                                                         >  2:206405/1‑134 (MQ=255)
                                      caaaggtaatgaAATCATATCTGTAGGCATTTCATCATTAGAAGCTGCAACGCAATAACGTGGTGCTTTTGAAGCAAATATTCAAAAATTAATCGCAGGTGTTAAATC‑TTCACAGCGTGCCGTACTATTCTTtg                                                                                                <  2:274933/134‑1 (MQ=255)
                                                gaAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATCCTTTGATGAAATCCa                                                                                      >  1:266141/1‑134 (MQ=255)
                                                  aaTTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATc                                                                                    <  1:185023/134‑1 (MQ=255)
                                                        ttCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTa                                                                              >  1:487811/1‑134 (MQ=255)
                                                         tCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGTTGTTCAATA‑ATATAAAAATGCCGTACTATTCTTTGATGAAAGACATCAAAatat                                                                             >  2:428755/1‑134 (MQ=255)
                                                                     tcatcaTTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGTATCACGTGc                                                                 >  1:247774/1‑134 (MQ=255)
                                                                     tcatcaTTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATACATCAAATAATCGGTTCAGGTga                                                                 >  1:134674/1‑133 (MQ=255)
                                                                        ttaatAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCcac                                                              <  2:582761/130‑1 (MQ=255)
                                                                        tcatTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCcac                                                              <  2:582760/134‑1 (MQ=255)
                                                                        tcatTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCcac                                                              >  2:539177/1‑134 (MQ=255)
                                                                        tcatTAGAAGCGGGAACGCAATACCTTGGTGCTGTTGCAGCCCCCCTTCAGTAATTAATCGACGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCcac                                                              <  1:573895/134‑1 (MQ=255)
                                                                           ttAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGCAAATCCTCAAAAACTAAGCGGAGCTG‑TAAATCACGCACATAACGCCGTACTATTCTTTGACGAAATCCATCAAATTATCGGTTCAGTCGCCACAgg                                                           <  2:90056/134‑1 (MQ=255)
                                                                           ttAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAgg                                                           <  1:250793/134‑1 (MQ=255)
                                                                           ttAGAAGCTGGAACGCAATATCGTGGTGCTGTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAgg                                                           <  2:552504/134‑1 (MQ=255)
                                                                             aGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGaa                                                         <  1:392180/134‑1 (MQ=255)
                                                                              gAATCTTGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAATTTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAg                                                        <  1:221794/134‑1 (MQ=255)
                                                                              gAAGTTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAg                                                        <  2:169394/134‑1 (MQ=255)
                                                                              gAAGCGGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAg                                                        <  2:168211/134‑1 (MQ=255)
                                                                                   tGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCTACAGGAAGTGAtt                                                   >  1:238249/1‑134 (MQ=255)
                                                                                   tGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGATCAGGTGCAACAGGAAGTGAtt                                                   >  1:532495/1‑134 (MQ=255)
                                                                                      aaCGCAATATCGTGGTGCTTTTGAAGAAAATCTTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTCATTAAg                                                >  1:180234/1‑134 (MQ=255)
                                                                                       aCGCAATATCGTGGTGTTTTTGAAGAAAATATTCAAAAATTAATCTTAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAgg                                               <  1:587150/134‑1 (MQ=255)
                                                                                        cGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATGGAAGGTGTTAAATC‑TTCCCAAAATGCCGTACTATTCTTTGATGAAATCCATCACATTATCGGTTCAGGTGCCACAGGACGTGCTTCAGGt                                              >  1:121919/1‑134 (MQ=255)
                                                                                             tatCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATAAAATAATCGGTTCAGTGGCAACAGGAAGTGATTAAGGAAGCaa                                         >  2:221437/1‑134 (MQ=255)
                                                                                             tatCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCAGTACTATTCTTTGATGAAATCCATCAAATTATCGCTTCAGGTGCCACAGGAAGTGATTCAGGTATCaa                                         >  2:73868/1‑134 (MQ=255)
                                                                                              atCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTAAGGTGCCACAGGAAGTGATTAAGGTAGCaaa                                        >  2:159412/1‑134 (MQ=255)
                                                                                              atCGTGGTGCGTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACGATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCaaa                                        <  2:159000/134‑1 (MQ=255)
                                                                                                cGTGGTGCTTTTCAAGAAAATACTCAAAAATTACTCGAAGGTGTTAAATC‑TTCACTAGATGCCGTACTATTCTTTGATGAAATCCATCCACTTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAgg                                      <  2:144440/134‑1 (MQ=255)
                                                                                                  tggtgCTTTTGAAGAAAATATTCAAAAATTAATCTTAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGt                                    <  2:492593/134‑1 (MQ=255)
                                                                                                    gtgCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTGAGGTAGCAAAGGGTTa                                  >  2:253887/1‑134 (MQ=255)
                                                                                                     tgCTTTTGAAGAAAATATTCAAAAATTAATTGTAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTAt                                 <  1:470874/134‑1 (MQ=255)
                                                                                                      gCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAGATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGATAGCAAAGGGTTATc                                >  2:300283/1‑134 (MQ=255)
                                                                                                         tttGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCCCAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGa                             >  1:554273/1‑134 (MQ=255)
                                                                                                         tttGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGa                             >  1:555332/1‑134 (MQ=255)
                                                                                                                     atTCAAAGATTTATTGAAGGTGTTAAATC‑TTCACAAAATGCCATACTATTCTTTGATGAAATCCATCAAATTAACGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAATGGTTATCTGATATTTTGAAAcc                 <  1:264342/134‑1 (MQ=255)
                                                                                                                        cAAAAATTAATCTTAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTCATCTGATATTTTGAAAccaga              >  2:7209/1‑131 (MQ=255)
                                                                                                                          aaaaTTAATCGAAGTTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGATATTTTGAAACCTGCAt            <  1:63951/134‑1 (MQ=255)
                                                                                                                              ttAATCGAATGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGATATTTTGAAACCTGCATTAAg        <  1:107383/134‑1 (MQ=255)
                                                                                                                                  tCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGATATTTTGAAACCTGCATTAAGTCgt    <  1:356344/134‑1 (MQ=255)
                                                                                                                                    gAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGATATTTTGAAACCTGCATTAAGTCgtgg  >  2:517646/1‑134 (MQ=255)
                                                                                                                                    gAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGATATTTTGAAACCTGCATTAAGTCgtgg  <  2:354418/134‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                     
GCACAGGCAATCGTTGAAGGAAATGTACCAGCAGCAATCAAAGACAAAGAAATTATTTCTGTAGACATTTCATCATTAGAAGCTGGAACGCAATATCGTGGTGCTTTTGAAGAAAATATTCAAAAATTAATCGAAGGTGTTAAATC‑TTCACAAAATGCCGTACTATTCTTTGATGAAATCCATCAAATTATCGGTTCAGGTGCCACAGGAAGTGATTCAGGTAGCAAAGGGTTATCTGATATTTTGAAACCTGCATTAAGTCGTGG  >  USA300TCH1516_ALE/2685758‑2686023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑