Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,762,304 C→A 9.9% T94N (ACC→AAC)  yfjQ → CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,762,3040CA 9.9% 1922.5 / 147.9 585T94N (ACC→AAC) yfjQCP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (326/200);  new base A (49/10);  total (375/210)
Fisher's exact test for biased strand distribution p-value = 1.44e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

Only 100 of 595 total aligned reads displayed.

TACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTG  >  CP009273/2762238‑2762371
                                                                  |                                                                   
 aCGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTAcc                                                                    <  1:35248502/67‑1 (MQ=255)
  cGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCgg                                                                  <  1:14711083/68‑1 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 >  1:9717956/1‑68 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 >  1:19987496/1‑68 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 <  1:16905441/68‑1 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 <  1:4450918/68‑1 (MQ=255)
    tGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTa                                                                >  1:21518317/1‑68 (MQ=255)
     gACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaa                                                               >  1:6096671/1‑68 (MQ=255)
     gACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaa                                                               >  1:20164607/1‑68 (MQ=255)
     gACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaa                                                               >  1:6554061/1‑68 (MQ=255)
       cccccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAAc                                                             >  1:17279396/1‑68 (MQ=255)
         cccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAg                                                           >  1:29984880/1‑68 (MQ=255)
         cccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAg                                                           >  1:7621365/1‑68 (MQ=255)
           cgtcgtcgtGAGCATACTAAGCATATGCTGCCCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGt                                                         <  1:32973487/68‑1 (MQ=255)
              cgtcgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTcc                                                      >  1:28300957/1‑68 (MQ=255)
                  gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                  <  1:20849463/68‑1 (MQ=255)
                      tcATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAAtt                                               <  1:12559011/66‑1 (MQ=255)
                      gCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAAtt                                               <  1:25854650/67‑1 (MQ=255)
                      gCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTa                                              >  1:13986759/1‑68 (MQ=255)
                        aTACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACACGTTCCGGAAATTa                                              <  1:36143109/66‑1 (MQ=255)
                         tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                  <  1:1587402/61‑1 (MQ=255)
                         tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                             >  1:16042058/1‑66 (MQ=255)
                           cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                          >  1:36712695/1‑67 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                          >  1:32462362/1‑66 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                          >  1:19683551/1‑66 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:4076359/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:13227282/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:26802737/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:13426380/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:32255920/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:18519850/68‑1 (MQ=255)
                             aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                                        <  1:10650072/64‑1 (MQ=255)
                             aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                                        <  1:503113/64‑1 (MQ=255)
                             aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                                        <  1:22596190/64‑1 (MQ=255)
                              aGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCtt                                      >  1:10268429/1‑68 (MQ=255)
                              aGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCtt                                      >  1:33607625/1‑68 (MQ=255)
                               gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:24805616/1‑68 (MQ=255)
                               acATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTa                                     >  1:34765993/2‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:11723600/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:34381639/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:35979772/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:27593488/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:2501108/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:20572606/1‑68 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:26310310/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:30470906/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:34133907/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:6974892/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:8560515/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:24565398/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:35586147/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:23568613/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:23403951/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:15586074/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:22258793/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGCAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCtaa                                     >  1:3862718/1‑65 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:25617469/1‑66 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                   <  1:16403554/68‑1 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                   <  1:15003050/68‑1 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                   <  1:16789092/68‑1 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                   <  1:18093018/68‑1 (MQ=255)
                                  tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                                  <  1:3639688/68‑1 (MQ=255)
                                  tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                                  <  1:30890128/68‑1 (MQ=255)
                                  tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                                  <  1:23057566/68‑1 (MQ=255)
                                  aatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTCCTTAAc                                   >  1:29423744/2‑67 (MQ=255)
                                    tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                 >  1:8346460/1‑67 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:23863279/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:18293567/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:33240702/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:19404525/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAAATACCGGAAAACCGGTTCCGGAAATTAACCTGCTTAActcac                               >  1:5735920/1‑66 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:29571947/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:13027205/1‑67 (MQ=255)
                                       tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCAc                             >  1:21800946/1‑68 (MQ=255)
                                       tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCAc                             >  1:31785292/1‑68 (MQ=255)
                                        gcgcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACg                            <  1:18935074/68‑1 (MQ=255)
                                           ccTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg                         >  1:8950224/1‑68 (MQ=255)
                                             tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                       <  1:12342616/68‑1 (MQ=255)
                                             tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                       <  1:1090152/68‑1 (MQ=255)
                                              aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                      <  1:37037686/68‑1 (MQ=255)
                                              aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                      <  1:1003428/68‑1 (MQ=255)
                                               cGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                      >  1:26531393/1‑67 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:24222421/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:11276823/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:27155470/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:7278477/68‑1 (MQ=255)
                                                    ggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 >  1:27036776/1‑67 (MQ=255)
                                                     gAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTc               >  1:19148707/1‑68 (MQ=255)
                                                      aGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCCCCAGTTCg              >  1:2923817/1‑68 (MQ=255)
                                                      aGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCg              >  1:4719760/1‑68 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt             <  1:25319879/66‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa            <  1:14528592/67‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa            <  1:934027/67‑1 (MQ=255)
                                                          gCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTAc           <  1:35059019/67‑1 (MQ=255)
                                                          gCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTAc           <  1:31470148/67‑1 (MQ=255)
                                                               ttACCGGTAAACAGGTTCCGGAAAATATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGAt      >  1:28614353/1‑67 (MQ=255)
                                                                tACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGAtgc    <  1:33448114/68‑1 (MQ=255)
                                                                tACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGAt      >  1:5438967/1‑66 (MQ=255)
                                                                 aCCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGAtgct   <  1:2900084/68‑1 (MQ=255)
                                                                  ccGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGAtgctg  <  1:22034622/68‑1 (MQ=255)
                                                                  |                                                                   
TACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTG  >  CP009273/2762238‑2762371

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: ‑