Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,608,829 C→T 8.5% intergenic (‑680/+150) USA300HOU_2470 ← / ← USA300HOU_2471 dehydrogenase/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,608,8290CT 8.5% 172.1 / 5.0 59intergenic (‑680/+150)USA300HOU_2470/USA300HOU_2471dehydrogenase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (23/31);  new base T (3/2);  total (26/33)
Fisher's exact test for biased strand distribution p-value = 6.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.51e-01

CAAGTTGAAAATGAAGGATTCTAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGGTAGTAATCATTG  >  CP000730/2608696‑2608968
                                                                                                                                     |                                                                                                                                           
aaaGTTGAAAATGAAGGATTCTAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACGTCCTGTATTGGATGTGGCtt                                                                                                                                      <  2:284407/140‑1 (MQ=255)
  aGTTGAAAATGAAGGATTCTAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCtttt                                                                                                                                    <  1:380386/141‑1 (MQ=255)
          aTGAAGGATTCTAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGt                                                                                                                            >  1:618727/1‑141 (MQ=255)
               ggATTCTAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAg                                                                                                                       <  2:140282/141‑1 (MQ=255)
                 aTTCTAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGAt                                                                                                                     <  1:447710/141‑1 (MQ=255)
                     tAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTtgt                                                                                                                 <  1:474150/141‑1 (MQ=255)
                      aaTATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTtgtg                                                                                                                >  1:11140/1‑141 (MQ=255)
                      aaTATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTtgtg                                                                                                                >  1:93252/1‑141 (MQ=255)
                      aaTATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTtgtg                                                                                                                <  2:588508/141‑1 (MQ=255)
                       atatCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCATTCCAGATTTGTgg                                                                                                               >  1:690086/1‑141 (MQ=255)
                        tatCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTggg                                                                                                              >  1:708245/1‑141 (MQ=255)
                                cGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAgg                                                                                                      <  2:346854/141‑1 (MQ=255)
                                 gTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAggg                                                                                                     <  1:446643/141‑1 (MQ=255)
                                 gTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAggg                                                                                                     <  1:647469/141‑1 (MQ=255)
                                  tttATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGATTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGGTAGGGt                                                                                                    >  2:359773/1‑141 (MQ=255)
                                       atataGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACt                                                                                               <  1:426750/141‑1 (MQ=255)
                                        tataGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACtt                                                                                              <  1:410176/141‑1 (MQ=255)
                                                  aTGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAggg                                                                                    <  2:57960/141‑1 (MQ=255)
                                                     aTAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTc                                                                                 >  1:641913/1‑141 (MQ=255)
                                                          aTTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGccc                                                                            <  1:72445/141‑1 (MQ=255)
                                                                    tAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTc                                                                  <  2:417279/141‑1 (MQ=255)
                                                                     aaaTCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTcgttggtgag                                                                 <  2:23887/141‑10 (MQ=255)
                                                                     aaaTCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCa                                                                 <  2:636226/141‑1 (MQ=255)
                                                                      aaTCTTATAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCAc                                                                >  2:584106/1‑141 (MQ=255)
                                                                           tGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACg                                                           <  1:645086/141‑1 (MQ=255)
                                                                            gTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGa                                                          >  2:21999/1‑141 (MQ=255)
                                                                            gTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGa                                                          <  2:334700/141‑1 (MQ=255)
                                                                                 tAATCNTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCa                                                     <  1:33185/141‑1 (MQ=255)
                                                                                 tAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCa                                                     >  2:220551/1‑141 (MQ=255)
                                                                                   aTCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAg                                                   >  2:242661/1‑141 (MQ=255)
                                                                                         ttAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGCGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACat                                             >  1:579751/1‑141 (MQ=255)
                                                                                           aaaaaTAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACatca                                           >  1:72660/1‑141 (MQ=255)
                                                                                            aaaaTAATATAAGTATGACTAAAGCCACATCCAATATAAGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGAGTTTGCTCTCAATTGCTAACCAAAGAGGGCAAGTTACatcaa                                          >  2:307712/1‑141 (MQ=255)
                                                                                                taataTAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATcac                                      <  1:630083/141‑1 (MQ=255)
                                                                                                   tataAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACt                                   <  1:31401/141‑1 (MQ=255)
                                                                                                   tataAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACt                                   <  1:486071/141‑1 (MQ=255)
                                                                                                   tataAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACt                                   <  1:267437/141‑1 (MQ=255)
                                                                                                    ataAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACtt                                  <  2:93947/141‑1 (MQ=255)
                                                                                                       aGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCaa                               >  1:142598/1‑141 (MQ=255)
                                                                                                       aGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCaa                               >  1:544448/1‑141 (MQ=255)
                                                                                                           tGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTgc                           <  2:582894/141‑1 (MQ=255)
                                                                                                              cTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATGTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTgccgc                        <  2:677375/141‑1 (MQ=255)
                                                                                                               tAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTgccgcc                       >  1:340331/1‑141 (MQ=255)
                                                                                                               tAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTgccgcc                       >  1:272490/1‑141 (MQ=255)
                                                                                                                aaaGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGccgccg                      >  1:614689/1‑141 (MQ=255)
                                                                                                                aaaGCCACATCCAATATAGGACGTGGCTTGTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCGATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGccgccg                      <  2:347964/141‑1 (MQ=255)
                                                                                                                 aaGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGa                     >  2:178564/1‑141 (MQ=255)
                                                                                                                    ccACGTCCTATATTGGATGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCaa                                                             <  2:547813/98‑1 (MQ=38)
                                                                                                                    ccACGTCCTATATTGGATGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCaa                                                             >  1:547813/1‑98 (MQ=38)
                                                                                                                       cgtcctatatTGGATGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCGCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAggg               >  1:136760/7‑141 (MQ=255)
                                                                                                                          ccAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGgta            <  2:693130/141‑1 (MQ=255)
                                                                                                                           ctatatTGGATGAGGCTTTTAGTATCGTTCCAGATTTGATGGGAGAGAGGGTTTACTTGATGAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCACGGTACATCAATCACACTTCAATTGCCGCCGGCTTGGGgtag           >  2:242793/3‑141 (MQ=255)
                                                                                                                            aaTATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGgtagt          <  1:220551/141‑1 (MQ=255)
                                                                                                                            aaTATAGGACGTGGCTTTTAGGATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGgtagt          <  1:358978/141‑1 (MQ=255)
                                                                                                                             atatAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGgtagta         <  2:449838/141‑1 (MQ=255)
                                                                                                                                  ggACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGGTAGTAATCAt    >  2:310419/1‑141 (MQ=255)
                                                                                                                                  ggACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGGTAGTAATCAt    >  1:225241/1‑141 (MQ=255)
                                                                                                                                  ggACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGGTAGTAATCAt    >  1:695611/1‑141 (MQ=255)
                                                                                                                                    aCGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGGTAGTAATCATTg  <  2:641913/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                           
CAAGTTGAAAATGAAGGATTCTAATATCATTTCGTTTATATATAGCAGACATGATAGAATTTTATATGTAAATCTTGTAGGTAATCGTTTTAAAAATAATATAAGTATGACTAAAGCCACATCCAATATAGGACGTGGCTTTTAGTATCGTTCCAGATTTGTGGGGAGTTAGGGTTTACTTAATTAAAGGGGTCTGCCCTCAATTGCTCACCAACGAGGGCAAGTTACATCAATCACACTTCAATTGCCGCCGACTAGGGGTAGTAATCATTG  >  CP000730/2608696‑2608968

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑