Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,762,304 C→A 10.2% 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
*CP0092732,762,3040CA10.2% 2042.0 / 166.3 615T94N (ACC→AAC) yfjQCP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (328/224);  new base A (56/7);  total (384/231)
Fisher's exact test for biased strand distribution p-value = 1.63e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

Only 100 of 631 total aligned reads displayed.

TACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTG  >  CP009273/2762238‑2762371
                                                                  |                                                                   
 aCGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTAcc                                                                    <  1:15215867/67‑1 (MQ=255)
  cGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCgg                                                                  <  1:15938432/68‑1 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGGAAATTACCGGt                                                                 >  1:11078389/1‑68 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 >  1:2931226/1‑68 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 >  1:11450201/1‑68 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 >  1:8894107/1‑68 (MQ=255)
   gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                                 >  1:17598364/1‑68 (MQ=255)
    tGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTa                                                                >  1:16352706/1‑68 (MQ=255)
     gACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaa                                                               <  1:27934808/68‑1 (MQ=255)
         cccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAg                                                           >  1:6076309/1‑68 (MQ=255)
              cgtcgtTAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTcc                                                      <  1:33947493/68‑1 (MQ=255)
                  gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                  <  1:25997970/68‑1 (MQ=255)
                  gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGCaa                                                  <  1:25088336/68‑1 (MQ=255)
                  gtGAGCATACTAAGCATATCCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                  <  1:34182949/68‑1 (MQ=255)
                          aCTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                             >  1:28690453/1‑65 (MQ=255)
                          aCTAAGCATATGCTGCGCCTACGTCGGGAGGGGAAAATTACCGGTAAACAGGTTCCGGAAATTAt                                             >  1:26302821/1‑65 (MQ=255)
                           cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                          >  1:31355089/1‑67 (MQ=255)
                           cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                          >  1:534547/1‑67 (MQ=255)
                           cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                          >  1:19373950/1‑67 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:29584153/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:3185385/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:185853/68‑1 (MQ=255)
                            tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                        <  1:13479558/68‑1 (MQ=255)
                             aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                                       >  1:10303445/1‑68 (MQ=255)
                             aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                                       >  1:5635965/1‑68 (MQ=255)
                             aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                                       >  1:31541674/1‑68 (MQ=255)
                              aGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTAcc                                                                    <  1:20014163/38‑1 (MQ=255)
                               gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:27074642/1‑68 (MQ=255)
                               gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:10034764/1‑68 (MQ=255)
                               gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:6589632/1‑68 (MQ=255)
                               acATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTa                                     >  1:16625383/2‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:30851418/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:20514560/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:1781363/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:19014080/1‑68 (MQ=255)
                                cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                    >  1:32528368/1‑68 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:27745126/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:16921040/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:33494169/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:8035364/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:11171839/1‑67 (MQ=255)
                                cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTACGGAAATTATCCTGCTTa                                     >  1:32257214/1‑67 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:19736411/1‑66 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                     >  1:22592360/1‑66 (MQ=255)
                                 atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                   <  1:14584906/68‑1 (MQ=255)
                                  tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                                  <  1:2891958/68‑1 (MQ=255)
                                    tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                 >  1:9208585/1‑67 (MQ=255)
                                    tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                 >  1:14940136/1‑67 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:12680870/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:30200880/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:12185400/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:18059418/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:18457913/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:33117937/1‑68 (MQ=255)
                                     gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:26733988/1‑68 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActcgc                               >  1:20975141/1‑65 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:31203378/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:7815087/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:5063764/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:9800992/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:11719193/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                               >  1:14234876/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATACTGCATAACtctc                               >  1:13044381/1‑67 (MQ=255)
                                      ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGGTCCGGAAATTATCCTGCTTAACtctc                               >  1:13701439/1‑67 (MQ=255)
                                       tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCa                              <  1:23606634/67‑1 (MQ=255)
                                       tgcGCCTACGGCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCAc                             >  1:25637414/1‑68 (MQ=255)
                                        gcgcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACg                            <  1:22890522/68‑1 (MQ=255)
                                          gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                          >  1:28437337/1‑68 (MQ=255)
                                          gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                          >  1:8420731/1‑68 (MQ=255)
                                          gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAACTATCCTGCTTAACTCTCACGa                           <  1:24897543/67‑1 (MQ=255)
                                            cTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg                         >  1:34628954/1‑67 (MQ=255)
                                            cTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg                         <  1:23180613/67‑1 (MQ=255)
                                             tccGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                       <  1:23939554/66‑1 (MQ=255)
                                             tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                       <  1:26454329/68‑1 (MQ=255)
                                             tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                       <  1:6909918/68‑1 (MQ=255)
                                             tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                       <  1:171632/68‑1 (MQ=255)
                                             tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                       <  1:4451475/68‑1 (MQ=255)
                                              aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                      <  1:30599487/68‑1 (MQ=255)
                                              aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                      <  1:21472924/68‑1 (MQ=255)
                                              aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                      <  1:28275756/68‑1 (MQ=255)
                                                 tCGGGAGGGGCAAATTACCTGTAAACAGGTACCGGAATTTATCCTGCTTAACTCTCACGATGGCACCa                   >  1:20167976/1‑68 (MQ=21)
                                                 tCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCa                   >  1:24646520/1‑68 (MQ=255)
                                                 tCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTAACGATGGCACCa                   >  1:7358857/1‑68 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:10569488/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:402710/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:10825965/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:29907556/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:15542069/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:20701236/68‑1 (MQ=255)
                                                   gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                 <  1:3573912/68‑1 (MQ=255)
                                                      aGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCg              >  1:26847937/1‑68 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt             <  1:21916818/66‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt             <  1:17251444/66‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt             <  1:22075850/66‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt             <  1:26645071/66‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa            <  1:25451937/67‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa            <  1:8757092/67‑1 (MQ=255)
                                                         ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa            <  1:9407001/67‑1 (MQ=255)
                                                          gCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTAc           <  1:6374965/67‑1 (MQ=255)
                                                          gCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTAc           <  1:21262097/67‑1 (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: ‑