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% 2103.9 / 172.6 645P99P (CCG→CCT) yfjQCP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (293/289);  new base T (55/7);  total (349/296)
Fisher's exact test for biased strand distribution p-value = 1.79e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.28e-01

Only 100 of 646 total aligned reads displayed.

CGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGTTCAGG  >  CP009273/2762255‑2762386
                                                                 |                                                                  
cgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGa                                                                  >  1:11894630/1‑68 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTCCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:21582794/68‑1 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:26358640/68‑1 (MQ=255)
 gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGCaa                                                                 <  1:25088336/68‑1 (MQ=255)
 gtGAGCATACAAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                                                 <  1:11604433/68‑1 (MQ=255)
   gAGCATTCTCATAATATGCTGCTCATACGTCTTTATGGTCAAATTACCGGTAAACATGTTCCGGaa                                                                 <  1:4811327/66‑1 (MQ=255)
     gCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTa                                                             >  1:16796289/1‑68 (MQ=255)
       aTACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                                            >  1:25467685/1‑67 (MQ=255)
        tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                                            >  1:1514343/1‑66 (MQ=255)
         aCTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCTGTAAACAGGTTCCGGAAATTATCCt                                                         <  1:30015463/68‑1 (MQ=255)
          cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTg                                                        <  1:29177585/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:9648663/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:33905611/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:31424205/68‑1 (MQ=255)
           tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                                       <  1:16098467/68‑1 (MQ=255)
            aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                                                       <  1:27040753/64‑1 (MQ=255)
              gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:10034764/1‑68 (MQ=255)
              gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:12696702/1‑68 (MQ=255)
              gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:20130125/1‑68 (MQ=255)
              acATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTa                                                    <  1:19828719/67‑1 (MQ=255)
              acATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCACGAAGTTCCTGAAATTATCCTGCTTa                                                    >  1:5137769/2‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGGAATTATCCTGCTTaa                                                   >  1:24820268/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:32528368/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:4188290/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:6671434/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:23690893/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:19571084/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:19175032/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:31771890/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:30905236/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:28090882/1‑68 (MQ=255)
               cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                                                   >  1:26820894/1‑68 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:8035364/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:29719747/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:23101407/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:3351933/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:16562293/1‑67 (MQ=255)
               cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                                    >  1:26675927/1‑67 (MQ=255)
                atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                                  <  1:14583762/68‑1 (MQ=255)
                atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                                  <  1:6974307/68‑1 (MQ=255)
                 tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                                                 <  1:10850017/68‑1 (MQ=255)
                 tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                                                  >  1:1538417/1‑67 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGTTTCAGGAAATTATCCTGCTTAActc                                                >  1:20404366/1‑67 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActct                                               <  1:8373956/68‑1 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                                >  1:53538/1‑67 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                                >  1:13659459/1‑67 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                                >  1:8758454/1‑67 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                                >  1:31237878/1‑67 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                                >  1:18477752/1‑67 (MQ=255)
                   tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                                                >  1:21373711/1‑67 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActcac                                              >  1:17707702/1‑66 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:7452361/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:33117937/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:34863210/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:8940982/1‑68 (MQ=255)
                    gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATACTGCTTAACtctc                                              >  1:13787432/1‑68 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGTTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCa                                             >  1:3791757/1‑68 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:7815087/1‑67 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:27800297/1‑67 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:22042334/1‑67 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                                              >  1:1812363/1‑67 (MQ=255)
                     ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATACTGCATAACtctc                                              >  1:13044381/1‑67 (MQ=255)
                       gcgcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACg                                           <  1:23315365/68‑1 (MQ=255)
                         gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAACTATCCTGCTTAACTCTCACGa                                          <  1:24937687/67‑1 (MQ=255)
                             aCGTCGGGAGGGGCAAATTACCGGTTAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                                     <  1:26475924/68‑1 (MQ=255)
                             aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                                     <  1:30599487/68‑1 (MQ=255)
                              cGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                                     >  1:11301362/1‑67 (MQ=255)
                              cGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                                     >  1:2838349/1‑67 (MQ=255)
                                 cGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAg                                 <  1:26206787/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:11094361/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:20690298/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:10569488/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:22744163/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:28594722/68‑1 (MQ=255)
                                  gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:5713810/68‑1 (MQ=255)
                                  gggAGGGGCAAATAACCGGGAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt                                <  1:29434922/68‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt                            <  1:17251444/66‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt                            <  1:25806224/66‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt                            <  1:30316689/66‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt                            <  1:28910426/66‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt                            <  1:9301132/66‑1 (MQ=255)
                                        ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa                           <  1:6160433/67‑1 (MQ=255)
                                         gCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTAc                          <  1:6374965/67‑1 (MQ=255)
                                                aCCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGAtgct                  <  1:21034899/68‑1 (MQ=255)
                                                   ggTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGcc               >  1:15623425/1‑68 (MQ=255)
                                                   ggTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGcc               >  1:17085037/1‑68 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:10281200/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:22293120/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:20941664/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:34246912/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:18768511/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:12136377/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:14870994/68‑1 (MQ=255)
                                                      aaaCAGGTTCCGGAAATTATCCTGCTTAACTCTAACGATGGCACCAGTTCGTACCAGATGCTGCCggg            <  1:27333168/68‑1 (MQ=255)
                                                           ggTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCTCCAGTTCGTACCAGATGCTGCCGGGCATGt       >  1:178723/1‑68 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:13338028/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:34567699/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:24289194/66‑1 (MQ=255)
                                                             ttCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:32195386/66‑1 (MQ=255)
                                                             atCCGCAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGATGCTGCCGGGCATGt       <  1:14231059/65‑1 (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: ‑