Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 887,393 T→A 5.5% intergenic (‑54/‑30) ybjJ ← / → rcdA putative drug efflux MFS transporter, inner membrane protein/transcriptional regulator of csgD and ybiJI; autoregulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913887,3930TA 5.5% 257.2 / 2.9 70intergenic (‑54/‑30)ybjJ/rcdAputative drug efflux MFS transporter, inner membrane protein/transcriptional regulator of csgD and ybiJI; autoregulator
Reads supporting (aligned to +/- strand):  ref base T (33/33);  new base A (2/2);  total (35/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGACGCCATTAACAGGCCTGGCAAAAAGAAGAACATAAACAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGAATACATGCT  >  NC_000913/887249‑887506
                                                                                                                                                |                                                                                                                 
cgtaCGCCATTAACAGGCCTGGCAAAAAGAAGAACATAAACAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGt                                                                                                                <  3:199870/145‑1 (MQ=255)
         ttAACAGGCCTGGCAAAAAGAAGAACATAAACAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTg                                                                                                       >  4:767631/1‑148 (MQ=255)
                  cTGGCAAAAAGAAGAACATAAACAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCagagagag                                                                                              <  3:767631/148‑1 (MQ=255)
                                    tAAACAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAAtt                                                                                                        >  3:1130343/1‑120 (MQ=255)
                                    tAAACAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAAtt                                                                                                        <  4:1130343/120‑1 (MQ=255)
                                        cAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAAt                                                                                                         <  4:177821/115‑1 (MQ=255)
                                        cAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAAt                                                                                                         >  3:177821/1‑115 (MQ=255)
                                        cAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGAc                                                                                      <  2:380098/134‑1 (MQ=255)
                                        cAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGAc                                                                                      >  1:380098/1‑134 (MQ=255)
                                          gcgcCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTg                                                                                                                 <  1:237837/105‑1 (MQ=255)
                                          gcgcCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTg                                                                                                                 >  2:237837/1‑105 (MQ=255)
                                               cAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACAAATGTAcaca                                                                                                           >  2:913477/1‑106 (MQ=255)
                                               cAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACAAATGTAcaca                                                                                                           <  1:913477/106‑1 (MQ=255)
                                                 ggTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCag                                                                                                    <  2:641914/111‑1 (MQ=255)
                                                 ggTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCag                                                                                                    >  1:641914/1‑111 (MQ=255)
                                                   ttCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACAtt                                                                                                                   <  4:1107491/94‑1 (MQ=255)
                                                   ttCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACAtt                                                                                                                   >  3:1107491/1‑94 (MQ=255)
                                                       gCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTg                                                                                                                 >  2:540385/1‑92 (MQ=255)
                                                       gCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTg                                                                                                                 <  1:540385/92‑1 (MQ=255)
                                                          tttCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCgaga                                                      >  2:1030061/1‑148 (MQ=255)
                                                           ttCAATGCATTACGTGAAGAATTTACGTTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACAtt                                                                                                                   <  1:916633/86‑1 (MQ=255)
                                                           ttCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGTAAGACAACATTAGCAAGGTTGTGTACAtt                                                                                                                   >  2:916633/1‑86 (MQ=255)
                                                              aaTGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCgcgc                                                                           <  3:475405/123‑1 (MQ=255)
                                                              aaTGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCgcgc                                                                           >  4:475405/1‑123 (MQ=255)
                                                              aaTGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGaaaaa                                                  <  1:1030061/148‑1 (MQ=255)
                                                               aTGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGaaaaaa                                                 >  3:129012/1‑148 (MQ=255)
                                                                 gCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCagagaga                                                                                               <  4:292516/100‑1 (MQ=255)
                                                                 gCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCagagaga                                                                                               >  3:292516/1‑100 (MQ=255)
                                                                   aTTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTAt                                             <  4:129012/148‑1 (MQ=255)
                                                                           aagaaTTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGt                                                                                                                <  3:92049/73‑1 (MQ=255)
                                                                           aagaaTTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGt                                                                                                                >  4:92049/1‑73 (MQ=255)
                                                                                       tCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTcgcg                                                                            >  3:336052/1‑97 (MQ=255)
                                                                                       tCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTcgcg                                                                            <  4:336052/97‑1 (MQ=255)
                                                                                       tCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATc                                                                   <  2:523086/106‑1 (MQ=255)
                                                                                       tCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATc                                                                   >  1:523086/1‑106 (MQ=255)
                                                                                        cATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCagagaga                                                                                               >  4:882685/1‑77 (MQ=255)
                                                                                        cATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCagagaga                                                                                               <  3:882685/77‑1 (MQ=255)
                                                                                        cATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTcg                                                                              <  3:802608/94‑1 (MQ=255)
                                                                                        cATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTcg                                                                              >  4:802608/1‑94 (MQ=255)
                                                                                        cATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTAt                                             >  1:117091/1‑127 (MQ=255)
                                                                                        cATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTAt                                             <  2:117091/127‑1 (MQ=255)
                                                                                             aTCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCagagaga                                                                                               <  3:672445/72‑1 (MQ=255)
                                                                                             aTCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCagagaga                                                                                               >  4:672445/1‑72 (MQ=255)
                                                                                                   tCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGaa                                                                                           >  4:1089816/1‑70 (MQ=255)
                                                                                                   tCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGaa                                                                                           <  3:1089816/70‑1 (MQ=255)
                                                                                                    cAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGaaa                                                                                          >  2:149503/1‑70 (MQ=255)
                                                                                                    cAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGaaa                                                                                          <  1:149503/70‑1 (MQ=255)
                                                                                                      aaaTAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGa           <  1:83066/147‑1 (MQ=255)
                                                                                                      aaaTAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGa           >  2:83066/1‑147 (MQ=255)
                                                                                                       aaTAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCTACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTg                       <  2:877078/134‑1 (MQ=255)
                                                                                                       aaTAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAAGTATCCAGGCCACGCTGGAGGCGGTg                       >  1:877078/1‑134 (MQ=255)
                                                                                                        aTAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGAATa        >  4:227627/1‑148 (MQ=255)
                                                                                                             aagaGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTcg                                                                              >  2:442156/1‑73 (MQ=255)
                                                                                                             aagaGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTcg                                                                              <  1:442156/73‑1 (MQ=255)
                                                                                                             aagaGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGAATACAt     <  3:1127608/146‑1 (MQ=255)
                                                                                                             aagaGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGAATACAt     >  4:1127608/1‑146 (MQ=255)
                                                                                                                  ggAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCgg                         <  1:106449/121‑1 (MQ=255)
                                                                                                                  ggAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCgg                         >  2:106449/1‑121 (MQ=255)
                                                                                                                  ggAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGAATACATGCt  >  4:416988/1‑144 (MQ=255)
                                                                                                                  ggAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGAATACATGCt  <  3:416988/144‑1 (MQ=255)
                                                                                                                   gAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCa                                                               >  1:321124/1‑82 (MQ=255)
                                                                                                                   gAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCa                                                               <  2:321124/82‑1 (MQ=255)
                                                                                                                     aGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGaaaaa                                                  <  1:923748/93‑1 (MQ=255)
                                                                                                                     aGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGaaaaa                                                  >  2:923748/1‑93 (MQ=255)
                                                                                                                     aGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTa                                              <  1:403544/97‑1 (MQ=255)
                                                                                                                     aGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTa                                              >  2:403544/1‑97 (MQ=255)
                                                                                                                           caTTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGaa          <  4:265821/127‑1 (MQ=255)
                                                                                                                           caTTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGaa          >  3:265821/1‑127 (MQ=255)
                                                                                                                                     attGTGTACAAATGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATcc                                           >  3:662414/2‑84 (MQ=255)
                                                                                                                                     attGTGTACAAATGTACACAATGGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGGGAAAAAATTATcc                                           <  4:662414/83‑1 (MQ=255)
                                                                                                                                          gtACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGaa                     >  1:161516/1‑101 (MQ=255)
                                                                                                                                          gtACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGaa                     <  2:161516/101‑1 (MQ=255)
                                                                                                                                             cATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCg                                                         >  4:520430/1‑62 (MQ=255)
                                                                                                                                             cATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCg                                                         <  3:520430/62‑1 (MQ=255)
                                                                                                                                                |                                                                                                                 
AGGACGCCATTAACAGGCCTGGCAAAAAGAAGAACATAAACAGCGCCCAGGTTCGGCGTTTCAATGCATTACGTGAAGAATTTACGGTCATAGATCACGTCAAAATAAGAAGAGGGAAGACAACATTAGCAAGGTTGTGTACATTTGTACACAATTGCAGAGAGAGGAAATGACATGCGTCGCGCTAACGATCCGCAACGGCGAGAAAAAATTATCCAGGCCACGCTGGAGGCGGTGAAACTTTACGGAATACATGCT  >  NC_000913/887249‑887506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: