Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 66,726 T→C 90.6% intergenic (‑194/‑148) araD ← / → araC pseudogene, truncated/ara regulon transcriptional activator; autorepressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00927366,7260TC90.6% 21118.3 / inf 6926intergenic (‑194/‑148)araD/araCpseudogene, truncated/ara regulon transcriptional activator; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (285/368);  new base C (2823/3440);  total (3113/3813)
Fisher's exact test for biased strand distribution p-value = 5.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 6955 total aligned reads displayed.

GCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGAAGAGC  >  CP009273/66659‑66792
                                                                   |                                                                  
   aataatCACTCTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTg                                                                 <  1:28764811/68‑1 (MQ=255)
    ataatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                <  1:3399910/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                >  1:24159787/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                >  1:6471510/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                >  1:19366098/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                               <  1:51483255/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                               <  1:11531252/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                               <  1:6994501/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                               <  1:37809884/68‑1 (MQ=255)
       atCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTc                                                              >  1:16224896/1‑67 (MQ=255)
       atCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTc                                                              >  1:25666165/1‑67 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            <  1:17376733/68‑1 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:35594703/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:45188038/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:13612544/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTGGGTccc                                                            >  1:25221945/1‑68 (MQ=255)
          aaTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:33037888/1‑66 (MQ=255)
          aaTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:48883961/1‑66 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCt                                                         <  1:10561043/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:30471297/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:58104889/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:47788803/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:7473719/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:21026610/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:13172704/68‑1 (MQ=255)
            tgtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                        >  1:26673723/1‑68 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCttt                                                       <  1:49391493/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCTTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:53627698/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:23565884/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:32540834/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:57593582/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:4084877/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:47343946/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:12046488/68‑1 (MQ=255)
               ggACTTTTCTGCCGTTATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:52108674/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:53113890/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:24628349/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:33515314/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTATGt                                                     <  1:21977832/68‑1 (MQ=255)
                gACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGtt                                                    >  1:50508231/1‑68 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                  >  1:52558907/1‑68 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                  >  1:4037060/1‑68 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                  <  1:34566960/68‑1 (MQ=255)
                    tttCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAg                                                >  1:50063616/1‑68 (MQ=255)
                      tCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGaa                                              >  1:29934545/1‑68 (MQ=255)
                      tCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGaa                                              <  1:3727637/68‑1 (MQ=255)
                         gCCGTGATTTTAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:39357282/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:46793466/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAAt                                             >  1:56619976/1‑66 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAAt                                             >  1:8887199/1‑66 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:27204435/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:27734143/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:12565864/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:38388539/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:18367464/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACCCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAAt                                             >  1:43451033/1‑66 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:39873540/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:3206352/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:7983079/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:55601411/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:21510404/67‑1 (MQ=255)
                            gTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCttt                                        <  1:42412664/68‑1 (MQ=255)
                              gATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTta                                      <  1:36712190/68‑1 (MQ=255)
                              gATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTta                                      <  1:26226728/68‑1 (MQ=255)
                                ttATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTtaat                                    >  1:54030729/1‑68 (MQ=255)
                                   taGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAg                                 <  1:35037261/68‑1 (MQ=255)
                                   taGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAg                                 <  1:17822766/68‑1 (MQ=255)
                                    aGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGc                                >  1:28220359/1‑68 (MQ=255)
                                    aGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGc                                >  1:8510535/1‑68 (MQ=255)
                                    aGACACTTTTGCTACGCGTTTTTGGCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGc                                >  1:56157026/1‑68 (MQ=255)
                                      acacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:45757182/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:44619739/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:15211650/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:18818438/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:16855460/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:48344245/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:55030836/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:22526151/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:11137873/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:3100331/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgc                              >  1:44105213/1‑67 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCGTGGTCCCGCTGTGTTACAGAATGCGTTTAATAAGCgg                              >  1:46249648/1‑68 (MQ=255)
                                         cTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGt                           >  1:38893987/1‑68 (MQ=255)
                                         cTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGt                           >  1:9512304/1‑68 (MQ=255)
                                          ttttGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGtt                          <  1:54497261/68‑1 (MQ=255)
                                           tttGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGtt                          >  1:29315954/1‑67 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                     <  1:51092566/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                     <  1:20455625/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                     <  1:1570543/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:42912633/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:41794712/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:4137329/1‑68 (MQ=255)
                                                  cgcgTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGttt                  >  1:19881414/1‑68 (MQ=255)
                                                   gcgTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTg                 <  1:14633148/68‑1 (MQ=255)
                                                   gcgTGTTTGTCCTGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTg                 <  1:14099913/68‑1 (MQ=255)
                                                     gTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTgg                <  1:10022590/67‑1 (MQ=255)
                                                        tttGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAg            <  1:5709677/68‑1 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTAGCGGTTTGGTTTGCgaga       >  1:22941521/1‑68 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgaga       >  1:36111803/1‑68 (MQ=255)
                                                                ggCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGagaaga    <  1:3155567/68‑1 (MQ=255)
                                                                   |                                                                  
GCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGAAGAGC  >  CP009273/66659‑66792

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑