Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 66,726 T→C 87.3% 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
*CP00927366,7260TC87.3% 6905.8 / inf 2470intergenic (‑194/‑148)araD/araCpseudogene, truncated/ara regulon transcriptional activator; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (151/162);  new base C (1013/1136);  total (1169/1301)
Fisher's exact test for biased strand distribution p-value = 7.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 2485 total aligned reads displayed.

GCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGAAGAGCC  >  CP009273/66659‑66793
                                                                   |                                                                   
gCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCt                                                                     <  1:8297251/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                 >  1:16155980/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                 >  1:15945812/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                 >  1:11864868/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                 >  1:14859203/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                 >  1:13815666/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTgg                                                                 >  1:29126604/1‑67 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                                <  1:570059/68‑1 (MQ=255)
     taatCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGt                                                                <  1:17188364/68‑1 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTccc                                                             >  1:23086377/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                             >  1:25296074/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                             >  1:26317800/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                             >  1:2438019/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                             >  1:1776792/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                             >  1:13086242/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                             >  1:10020546/1‑68 (MQ=255)
        tCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTccc                                                             >  1:2355715/1‑68 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCt                                                          <  1:2937930/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                          <  1:12758554/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                          <  1:26096291/68‑1 (MQ=255)
           aTGTGGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCt                                                          <  1:21128080/68‑1 (MQ=255)
            tgtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                         >  1:27377201/1‑68 (MQ=255)
            tgtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                         >  1:19049037/1‑68 (MQ=255)
            tgtgGACTTTTCTACCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCtt                                                         >  1:10254208/1‑68 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTTGTCCCGCttt                                                        <  1:20823075/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                        <  1:24673946/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCttt                                                        <  1:18192343/68‑1 (MQ=255)
             gtgGACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGATCCCGCttt                                                        <  1:28952662/68‑1 (MQ=255)
             gtgGACTTTTCTACCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCTGCttt                                                        <  1:21405429/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGt                                                      <  1:526595/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                      <  1:16917626/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                      <  1:15353029/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                      <  1:28226630/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                      <  1:92726/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                      <  1:21653728/68‑1 (MQ=255)
               ggACTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGt                                                      <  1:20280532/68‑1 (MQ=255)
                gACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGtt                                                     >  1:5001279/1‑68 (MQ=255)
                 aCTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGtt                                                     >  1:7925467/1‑67 (MQ=255)
                 aCTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGtt                                                     >  1:22784790/1‑67 (MQ=255)
                 aCTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGtt                                                     >  1:23850360/1‑67 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                   <  1:4711572/68‑1 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                   >  1:1215221/1‑68 (MQ=255)
                  cTTTTCTGCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTAc                                                   >  1:15653449/1‑68 (MQ=255)
                         gCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGc                                            <  1:2660419/68‑1 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAAt                                              >  1:6562057/1‑66 (MQ=255)
                         gCCGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGc                                            <  1:17419173/68‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                          >  1:20582630/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                          >  1:3366058/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCtt                                          >  1:2842344/1‑68 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                           <  1:13324105/67‑1 (MQ=255)
                           cGTGATTATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCt                                           <  1:28715824/67‑1 (MQ=255)
                                ttATAGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTtaat                                     >  1:23272959/1‑68 (MQ=255)
                                  ataGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTtaataa                                   <  1:27690234/68‑1 (MQ=255)
                                    aGACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGc                                 >  1:7330490/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                                >  1:11303983/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                                >  1:25798726/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                                >  1:7645962/1‑68 (MQ=255)
                                     gACACTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCg                                >  1:15159926/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:11113629/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:13504834/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:9481250/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:19757735/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:25560494/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:5467234/1‑68 (MQ=255)
                                      acacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:386791/1‑68 (MQ=255)
                                      acacTTATGCTACGCGTTTTTGTCATCGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               >  1:6916832/1‑68 (MQ=255)
                                       cacTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               <  1:3068235/67‑1 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                              <  1:3606193/68‑1 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                              <  1:7167034/68‑1 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCggg                              >  1:12425376/1‑68 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               <  1:11685135/67‑1 (MQ=255)
                                       cacTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgg                               <  1:2691694/67‑1 (MQ=255)
                                        acTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgggg                             <  1:29678810/68‑1 (MQ=255)
                                        acTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCgggg                             <  1:21951098/68‑1 (MQ=255)
                                         cTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGt                            >  1:27140790/1‑68 (MQ=255)
                                         cTTTTGCTACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGt                            <  1:25022892/68‑1 (MQ=255)
                                           tttGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGtt                           >  1:14143897/1‑67 (MQ=255)
                                              gctACGCGTTTTTGACATGGCCTTGCTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCg                       >  1:20054972/3‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                      <  1:10492335/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTTCAGGt                     >  1:6269564/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                      <  1:16390/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                      <  1:1850512/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCgg                      <  1:5978352/67‑1 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                     >  1:4187827/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                     >  1:1938150/1‑68 (MQ=255)
                                                tACGCGTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGt                     >  1:18771147/1‑68 (MQ=255)
                                                  cgcgTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGttt                   >  1:4446504/1‑68 (MQ=255)
                                                   gcgTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTg                  <  1:18018424/68‑1 (MQ=255)
                                                   gcgTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTg                  <  1:16667406/68‑1 (MQ=255)
                                                     gTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTgg                 <  1:810746/67‑1 (MQ=255)
                                                     gTTTTTGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTgg                 <  1:9681569/67‑1 (MQ=255)
                                                        tttGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTa              >  1:8698370/1‑67 (MQ=255)
                                                        tttGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAg             <  1:27981178/68‑1 (MQ=255)
                                                        tttGTCATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAg             <  1:22402957/68‑1 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgaga        <  1:2415121/68‑1 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgaga        >  1:14413721/1‑68 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgag         <  1:10760149/67‑1 (MQ=255)
                                                             cATGGCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCgag         <  1:22140827/67‑1 (MQ=255)
                                                                ggCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGagaaga     <  1:8542242/68‑1 (MQ=255)
                                                                ggCCTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGagaaga     <  1:9005824/68‑1 (MQ=255)
                                                                   |                                                                   
GCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGAAGAGCC  >  CP009273/66659‑66793

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: ‑