Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,762,287 T→C 6.7% R88R (CGT→CGC)  yfjQ → CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,762,2870TC 6.7% 1858.5 / 78.9 555R88R (CGT→CGC) yfjQCP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (345/167);  new base C (24/13);  total (370/185)
Fisher's exact test for biased strand distribution p-value = 7.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.10e-01

Only 100 of 561 total aligned reads displayed.

TTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACC  >  CP009273/2762220‑2762353
                                                                   |                                                                  
   ccTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCgg                                                                 >  1:4283538/1‑68 (MQ=255)
   ccTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCgg                                                                 >  1:6404774/1‑68 (MQ=255)
   ccTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCgg                                                                 >  1:7785961/1‑68 (MQ=255)
      gTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAg                                                              <  1:16852016/68‑1 (MQ=255)
        cAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAggg                                                            <  1:27907973/68‑1 (MQ=255)
            cacGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAgggg                                                           <  1:24230645/65‑1 (MQ=255)
            cacGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGc                                                          <  1:20787619/66‑1 (MQ=255)
            cacGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaa                                                        >  1:14349026/1‑68 (MQ=255)
             acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                       <  1:8936032/68‑1 (MQ=255)
             acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                       >  1:16417995/1‑68 (MQ=255)
             acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                       >  1:29808338/1‑68 (MQ=255)
                          ccccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTTCGTCGGGAGGGGCTAATTACCGGGAATCa                                          >  1:12099810/1‑68 (MQ=25)
                            ccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAgg                                        <  1:29123151/68‑1 (MQ=255)
                               tcgtcgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGtt                                      >  1:18730338/1‑67 (MQ=255)
                                   cgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGa                                 >  1:26104866/1‑68 (MQ=255)
                                   cgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGa                                 >  1:19081080/1‑68 (MQ=255)
                                    gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                <  1:27627530/68‑1 (MQ=255)
                                     tGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaaa                               >  1:23328500/1‑68 (MQ=255)
                                        gCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTa                            >  1:30941598/1‑68 (MQ=255)
                                           tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                           >  1:4210264/1‑66 (MQ=255)
                                           tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                           >  1:15490234/1‑66 (MQ=255)
                                             cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                        >  1:30072947/1‑67 (MQ=255)
                                             cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                        >  1:10054902/1‑67 (MQ=255)
                                             cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                        >  1:17935102/1‑67 (MQ=255)
                                             cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                        >  1:11371619/1‑67 (MQ=255)
                                              tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                      <  1:18388551/68‑1 (MQ=255)
                                              tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                      <  1:15728144/68‑1 (MQ=255)
                                              tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                      <  1:33318406/68‑1 (MQ=255)
                                              tAAGCATATGCTGCGCCTACGGCGGGAGGGGCAAATTACCGGTAAACAGGTTTCGGAAATTATCCTGc                      <  1:33665442/68‑1 (MQ=21)
                                               aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                      <  1:20230958/64‑1 (MQ=255)
                                               aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCt                     >  1:4805744/4‑68 (MQ=255)
                                               aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                     >  1:8150180/1‑68 (MQ=255)
                                                aGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGTAATTATACTGCtt                    >  1:34140997/1‑68 (MQ=255)
                                                 gCATATCCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:13198562/1‑68 (MQ=255)
                                                  cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                  >  1:19887705/1‑68 (MQ=255)
                                                  cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                  >  1:13967956/1‑68 (MQ=255)
                                                  cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                  >  1:26497361/1‑68 (MQ=255)
                                                  cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                  >  1:1513669/1‑68 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:32529350/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:11653901/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:2701474/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:26809866/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:28596817/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:25305116/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:17575252/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:21809673/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:5073050/1‑67 (MQ=255)
                                                  cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGGTCCGGAAATTATCCTGCTTa                   >  1:3722537/1‑67 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGTTAAACAGGTTCCGGAAATTATCCAGCTTa                   >  1:10852022/1‑66 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTaa                  <  1:5969043/67‑1 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:22893261/1‑66 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:24655138/1‑66 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:20387605/1‑66 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                   >  1:19507268/1‑66 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                 <  1:13354688/68‑1 (MQ=255)
                                                   atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                 <  1:25970949/68‑1 (MQ=255)
                                                    tatGCTGCGCCTACGTCTGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                <  1:3593854/68‑1 (MQ=255)
                                                    tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                 >  1:24901544/1‑67 (MQ=255)
                                                    tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                 >  1:5740525/1‑67 (MQ=255)
                                                      tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc               >  1:7097306/1‑67 (MQ=255)
                                                      tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc               >  1:31346482/1‑67 (MQ=255)
                                                      tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc               >  1:19325797/1‑67 (MQ=255)
                                                      tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc               >  1:33420592/1‑67 (MQ=255)
                                                      tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc               >  1:6627186/1‑67 (MQ=255)
                                                      tgctgcACCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc               >  1:978422/1‑67 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:30801940/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:12532202/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:12801894/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:21126739/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:22061508/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:34377669/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:33818588/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:29611470/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:29242106/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:32010066/1‑68 (MQ=255)
                                                       gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGATTAACtctc             >  1:32772016/1‑68 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTCCCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:14581571/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:11121851/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:9378806/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:31823986/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:11760219/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:7428873/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:23905936/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:16534433/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:4450746/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:12308943/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:7002654/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:2740468/1‑67 (MQ=255)
                                                        ctgcGCCTACGTCGGGAGGGGCAAACTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc             >  1:28118555/1‑67 (MQ=255)
                                                         tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCa            <  1:13015530/67‑1 (MQ=255)
                                                         tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCa            <  1:28461007/67‑1 (MQ=255)
                                                            gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGa         <  1:1612893/67‑1 (MQ=255)
                                                             ccTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg       >  1:22444155/1‑68 (MQ=255)
                                                              cTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg       <  1:5455293/67‑1 (MQ=255)
                                                               tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc     <  1:30576811/68‑1 (MQ=255)
                                                               tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc     <  1:15978563/68‑1 (MQ=255)
                                                               tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc     <  1:3930969/68‑1 (MQ=255)
                                                               tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc     <  1:21574119/68‑1 (MQ=255)
                                                                aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa    <  1:26370762/68‑1 (MQ=255)
                                                                aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa    <  1:10480971/68‑1 (MQ=255)
                                                                   |                                                                  
TTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACC  >  CP009273/2762220‑2762353

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: ‑