Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 66,726 T→C 68.4% 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
*CP00927366,7260TC68.4% 1536.7 / inf 1155intergenic (‑194/‑148)araD/araCpseudogene, truncated/ara regulon transcriptional activator; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (175/189);  new base C (369/418);  total (544/611)
Fisher's exact test for biased strand distribution p-value = 7.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 1165 total aligned reads displayed.

GCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGAAGAGC  >  CP009273/66659‑66792
                                                                   |                                                                  
    ataatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTgg                                                                <  1:6169897/68‑1 (MQ=255)
    ataatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTCTGCTACGCGTTTTTGTCATGGCCTTgg                                                                <  1:26602781/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGCTTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTgg                                                                >  1:37800378/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTgg                                                                >  1:18340310/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                >  1:4835697/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                               <  1:9669746/68‑1 (MQ=255)
       atCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTc                                                              >  1:13806554/1‑67 (MQ=255)
       atCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTc                                                              >  1:6785672/1‑67 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTccc                                                            >  1:29479045/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTccc                                                            >  1:1650332/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGAGTTTTTGGCATGGATTTGGAccc                                                            >  1:24728467/1‑68 (MQ=255)
         cAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCg                                                           <  1:34934074/68‑1 (MQ=255)
         cAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCg                                                           <  1:17287990/68‑1 (MQ=255)
          aaTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTccc                                                            >  1:29074429/1‑66 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         >  1:11930312/1‑68 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:36638394/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                         <  1:1215236/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGACCCGCt                                                         <  1:5275595/68‑1 (MQ=255)
            tgtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                        >  1:10774469/1‑68 (MQ=255)
            tgtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                        >  1:11634354/1‑68 (MQ=255)
            tgtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                        >  1:12588118/1‑68 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCttt                                                       <  1:20901241/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       >  1:8134728/1‑68 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:25793484/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:22535523/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:25117183/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:30201479/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       >  1:35805957/1‑68 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:37458676/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:38699149/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                       <  1:1475309/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGt                                                     <  1:8481128/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:18719153/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:16891134/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:7126391/68‑1 (MQ=255)
               ggACTTTGCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                     <  1:19343678/68‑1 (MQ=255)
                gACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTACCGCTTTGtt                                                    >  1:32689680/1‑68 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                  <  1:31749216/68‑1 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                  >  1:29883459/1‑68 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                  >  1:13458482/1‑68 (MQ=255)
                     ttCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGa                                               <  1:38939450/68‑1 (MQ=255)
                     ttCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGa                                               <  1:765639/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAAt                                             >  1:23406291/1‑66 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAAt                                             >  1:34420071/1‑66 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAAt                                             >  1:30906891/1‑66 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:11125182/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:27660126/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                           <  1:32297719/68‑1 (MQ=255)
                         gCCGTGATTATAGACACATTTGTTACGGGTTTTAGTCATGGCTTTCGTCCCGCTTTGTTACAGACTGc                                           <  1:4568012/68‑1 (MQ=255)
                           cgcgATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                          <  1:33298875/64‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:4376264/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGTTACGCGGTTTTGTCATGGCTTTGGGCCCGCTTTGTTACAGAATGCt                                          <  1:36892668/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:14186714/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:5075188/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:16123575/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:33978159/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:33148587/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                         >  1:20586202/1‑68 (MQ=255)
                              gATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCtttt                                       <  1:21311452/67‑1 (MQ=255)
                              gATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTta                                      <  1:31167303/68‑1 (MQ=255)
                                 tataGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTtaata                                   <  1:20310707/68‑1 (MQ=255)
                                 tataGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTtaata                                   <  1:10000664/68‑1 (MQ=255)
                                     gACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:30424524/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:26099478/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:8934713/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               >  1:33637957/1‑68 (MQ=255)
                                      acacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:36132296/1‑68 (MQ=255)
                                      acacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:15571145/1‑68 (MQ=255)
                                      acacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:32008363/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:15172398/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:17986629/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:28545685/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                              >  1:5793789/1‑68 (MQ=255)
                                       cacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                             <  1:25444904/68‑1 (MQ=255)
                                       cacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                             <  1:17554529/68‑1 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                             >  1:23060204/1‑68 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                             <  1:3836117/68‑1 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                             <  1:21918116/68‑1 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                               <  1:24062089/66‑1 (MQ=255)
                                        acTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgggg                            <  1:11466489/68‑1 (MQ=255)
                                        acTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgggg                            <  1:32881474/68‑1 (MQ=255)
                                        acTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgggg                            <  1:27124529/68‑1 (MQ=255)
                                         cTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGt                           <  1:38012480/68‑1 (MQ=255)
                                           tttGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGtt                          >  1:23712926/1‑67 (MQ=255)
                                             tgctACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTAcc                       <  1:4031036/65‑1 (MQ=255)
                                             tgctACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTAcc                       <  1:22141111/65‑1 (MQ=255)
                                              gctACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCg                      >  1:39169999/3‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:6403205/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:24307278/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:15838320/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                    >  1:27331729/1‑68 (MQ=255)
                                                   gcgTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTg                 <  1:35400576/68‑1 (MQ=255)
                                                   gcgTTTTTGTCATGGCCTTGGGCCCGCTTTGTTACAGACTGCTTTTAATAAGCGGGGTTACCGGTTTg                 <  1:9404487/68‑1 (MQ=255)
                                                     gTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTgg                <  1:34606395/67‑1 (MQ=255)
                                                          tGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCg          <  1:28317009/68‑1 (MQ=255)
                                                          tGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCg          >  1:10349447/1‑68 (MQ=255)
                                                             cATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgag        <  1:27899132/67‑1 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgag        <  1:12998630/67‑1 (MQ=255)
                                                                ggCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGagaaga    <  1:19037619/68‑1 (MQ=255)
                                                                  cTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGAagag   >  1:19789266/1‑67 (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: ‑