Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 66,726 T→C 56.0% 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
*CP00927366,7260TC56.0% 322.9 / inf 804intergenic (‑194/‑148)araD/araCpseudogene, truncated/ara regulon transcriptional activator; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (157/196);  new base C (208/242);  total (366/438)
Fisher's exact test for biased strand distribution p-value = 6.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 815 total aligned reads displayed.

GCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGAAGAGC  >  CP009273/66659‑66792
                                                                   |                                                                  
gCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCt                                                                    <  1:7067444/68‑1 (MQ=255)
gCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCt                                                                    <  1:30688167/68‑1 (MQ=255)
   aataatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTg                                                                 <  1:5807158/68‑1 (MQ=255)
   aataatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTg                                                                 <  1:5534046/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTATGCGTTTTTGTCATGGCTTTgg                                                                >  1:4536023/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGt                                                               <  1:32778599/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                               <  1:22434817/68‑1 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTAGGTccc                                                            >  1:29591390/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:6015911/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:28006747/1‑68 (MQ=255)
         cAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCg                                                           <  1:13011031/68‑1 (MQ=255)
          aaTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTccc                                                            >  1:11745357/1‑66 (MQ=255)
          aaTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:12020057/1‑66 (MQ=255)
          aaTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:3980673/1‑66 (MQ=255)
          aaTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                            >  1:17029855/1‑66 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCt                                                         <  1:30940606/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCt                                                         <  1:22006945/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCt                                                         <  1:22936849/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCt                                                         <  1:13510182/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         >  1:5221036/1‑68 (MQ=255)
            tgtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                        >  1:32372285/1‑68 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCttt                                                       <  1:7781889/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCttt                                                       <  1:14004596/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCttt                                                       <  1:6675046/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:29145121/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:18782545/68‑1 (MQ=255)
               gggcTTTTCTGCCGTGATTATAGACACTTCTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:23860847/65‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGt                                                     <  1:23729400/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGt                                                     <  1:9055300/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:111537/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:27710490/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:1076076/68‑1 (MQ=255)
                 aCTTTTCTGCCGTGATTAAAGCCACTTTTGCAACGAGATTTTGTCATGGCCTTGCTCACCCTTTGtt                                                    >  1:34454521/1‑67 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTAc                                                  <  1:748580/68‑1 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTAc                                                  >  1:17223089/1‑68 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTAc                                                  <  1:16795479/68‑1 (MQ=255)
                    tttCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAg                                                >  1:31582910/1‑68 (MQ=255)
                     ttCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGa                                               <  1:62471/68‑1 (MQ=255)
                      tCTGCCGTGATTATAGACACTTTTGTTACCCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGaa                                              >  1:8527650/1‑68 (MQ=255)
                      tCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGaa                                              >  1:31343706/1‑68 (MQ=255)
                         gCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:20775908/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:29879826/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:16255397/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:33218228/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:20129352/68‑1 (MQ=255)
                           cGTGATTATAGTCACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:24947533/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:18588251/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:16559716/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:31047738/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:2322157/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:19611438/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:17619925/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:9585876/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:10101955/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:9717442/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:13809912/67‑1 (MQ=255)
                             tGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtttt                                       >  1:30503800/1‑68 (MQ=255)
                              gATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTta                                      <  1:12761857/68‑1 (MQ=255)
                                    aGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGc                                >  1:33659746/1‑68 (MQ=255)
                                    aGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGc                                >  1:22230322/1‑68 (MQ=255)
                                     gACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCTCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:8149952/1‑68 (MQ=255)
                                     gACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:31883583/1‑68 (MQ=255)
                                     gACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:1159322/1‑68 (MQ=255)
                                     gACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:14771163/1‑68 (MQ=255)
                                     gACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:4842052/1‑68 (MQ=255)
                                     gACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:33849160/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:24155412/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:26660950/1‑68 (MQ=255)
                                      acacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:1048279/1‑68 (MQ=255)
                                      acacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:28789027/1‑68 (MQ=255)
                                      acacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:18192662/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:15921764/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:24601792/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:3717896/1‑68 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                             >  1:19882019/1‑68 (MQ=255)
                                        acTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgggg                            <  1:15434698/68‑1 (MQ=255)
                                         cTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGt                           >  1:14352432/1‑68 (MQ=255)
                                           tttGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTa                         <  1:30180160/68‑1 (MQ=255)
                                             tgctACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTAcc                       <  1:22712349/65‑1 (MQ=255)
                                              gctACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCg                      >  1:27558380/3‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:1935000/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:12356605/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:34172924/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                     <  1:28601974/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                     <  1:28317246/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                     <  1:25858741/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                     <  1:27127936/67‑1 (MQ=255)
                                                 aCGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCATTTAATAAGCGGGGTTACCGGtt                   <  1:177884/68‑1 (MQ=255)
                                                  cgcgTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGttt                  >  1:2614114/1‑68 (MQ=255)
                                                        tttGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAg            <  1:20539192/68‑1 (MQ=255)
                                                        tttGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAg            <  1:8865469/68‑1 (MQ=255)
                                                          tGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCg          <  1:2174136/68‑1 (MQ=255)
                                                          tGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGNTACCGGTTTGGTTAGCg          <  1:2134180/68‑1 (MQ=255)
                                                          tGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCg          <  1:25707186/68‑1 (MQ=255)
                                                          tGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCg          <  1:12506799/68‑1 (MQ=255)
                                                          tGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCg          >  1:34816899/1‑68 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgaga       >  1:18924386/1‑68 (MQ=255)
                                                                ggCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGagaaga    >  1:26881122/1‑68 (MQ=255)
                                                                ggCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGagaaga    <  1:32155942/68‑1 (MQ=255)
                                                                ggCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGagaaga    <  1:15105899/68‑1 (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: ‑