Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,762,320 G→T 9.6% P99P (CCG→CCT)  yfjQ → CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,762,3200GT 9.6% 1997.9 / 160.5 616P99P (CCG→CCT) yfjQCP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (292/263);  new base T (48/12);  total (341/275)
Fisher's exact test for biased strand distribution p-value = 3.37e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.95e-01

Only 100 of 616 total aligned reads displayed.

CGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGTTCAGG  >  CP009273/2762255‑2762386
                                                                 |                                                                  
cgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGa                                                                  <  1:25019031/68‑1 (MQ=255)
cgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGa                                                                  >  1:34876632/1‑68 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:29357111/68‑1 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:296782/68‑1 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:20849463/68‑1 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:13737249/68‑1 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:3814604/68‑1 (MQ=255)
  tGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTAACGGTAAACAGGTTCCGGaaa                                                                >  1:19433918/1‑68 (MQ=255)
       aTACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                                            <  1:19811091/67‑1 (MQ=255)
        tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                                            >  1:4417212/1‑66 (MQ=255)
         aCTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                                            >  1:31113095/1‑65 (MQ=255)
          cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                                         >  1:533892/1‑67 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                                         >  1:35617877/1‑66 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:24708069/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:32255920/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:13426380/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:13227282/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:26802737/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:10996108/68‑1 (MQ=255)
            aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                                                       <  1:503113/64‑1 (MQ=255)
            aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCt                                                      >  1:25478932/4‑68 (MQ=255)
             aGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCtt                                                     >  1:10268429/1‑68 (MQ=255)
             aGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCtt                                                     >  1:33607625/1‑68 (MQ=255)
              gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:32782061/1‑68 (MQ=255)
              acATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTa                                                    >  1:21715096/2‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:10807458/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:8358526/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:28529388/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:20438081/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:29167153/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:11723600/1‑68 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:5965967/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:8560515/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:23568613/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:23403951/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:22258793/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:34133907/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:15586074/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:16032928/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:19249605/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:16437649/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:16989675/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACACGTTCCGGAAATTATCCTGCTTa                                                    >  1:36031626/1‑67 (MQ=255)
                atatGCTGCGCCTACGTCGGGAGGGGCTAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:30666162/1‑66 (MQ=255)
                atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:9701255/1‑66 (MQ=255)
                atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:1908363/1‑66 (MQ=255)
                atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:12184708/1‑66 (MQ=255)
                atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                                  <  1:15003050/68‑1 (MQ=255)
                 tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                                                 <  1:12936914/68‑1 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:23863279/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:5676544/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:1467280/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:15816364/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:18261734/1‑68 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:6850811/1‑67 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:1772216/1‑67 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAAATACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACactc                                              >  1:21835511/1‑67 (MQ=255)
                       gcgcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACg                                           <  1:6235986/68‑1 (MQ=255)
                       gcgcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACg                                           <  1:18499026/68‑1 (MQ=255)
                         gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                                         >  1:27087110/1‑68 (MQ=255)
                         gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                                         >  1:33196554/1‑68 (MQ=255)
                         gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                                         <  1:9279834/68‑1 (MQ=255)
                           cTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg                                        >  1:25784640/1‑67 (MQ=255)
                            tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                                      <  1:26174265/68‑1 (MQ=255)
                             aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                                     <  1:1003428/68‑1 (MQ=255)
                              cgacGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACACTCACGATGGCa                                     >  1:26996696/4‑67 (MQ=255)
                              cGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                                     >  1:36800643/1‑67 (MQ=255)
                                  gggAGGTGCAAATTACCGGTAAACAGGTTCGGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:29487265/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACATGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:27428300/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:2450748/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:7278477/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:24222421/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:26506878/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:28786492/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:35285713/68‑1 (MQ=255)
                                   ggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCAGCTTAACTCTCACGATGGCACCAGt                                >  1:8828448/1‑67 (MQ=255)
                                     aGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCg                             >  1:4719760/1‑68 (MQ=255)
                                      ggggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCg                             <  1:36197636/67‑1 (MQ=255)
                                      ggggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt                            >  1:12468666/1‑68 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt                            <  1:25319879/66‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa                           <  1:18873064/67‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa                           <  1:14528592/67‑1 (MQ=255)
                                         gCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTAc                          <  1:35059019/67‑1 (MQ=255)
                                                  cGGTAAACAGGTTCCTGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGAtgctgc                <  1:11380900/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:23079330/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:33488109/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:10482520/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:22131470/68‑1 (MQ=255)
                                                        aCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCa          <  1:30234445/68‑1 (MQ=255)
                                                          aGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCTTg        >  1:7483419/1‑68 (MQ=255)
                                                          aGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGAAtt        >  1:16771348/1‑67 (MQ=255)
                                                             ttCCTGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:28023312/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:32480215/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:31830718/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:20046826/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:22579622/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:34411284/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:31533462/66‑1 (MQ=255)
                                                              tCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGTTc     <  1:3970413/67‑1 (MQ=255)
                                                              tCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGTTc     <  1:36405248/67‑1 (MQ=255)
                                                                 |                                                                  
CGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGTTCAGG  >  CP009273/2762255‑2762386

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: ‑