Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,762,299 A→T 6.3% Q92H (CAA→CAT)  yfjQ → CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,762,2990AT 6.3% 1968.9 / 80.8 580Q92H (CAA→CAT) yfjQCP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base A (331/212);  new base T (24/13);  total (355/225)
Fisher's exact test for biased strand distribution p-value = 7.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.98e-01

Only 100 of 611 total aligned reads displayed.

CACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGA  >  CP009273/2762232‑2762366
                                                                   |                                                                   
 acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                                    >  1:8315227/1‑68 (MQ=255)
       aCGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTAcc                                                               <  1:13159758/67‑1 (MQ=255)
       aCGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCg                                                              >  1:281990/1‑68 (MQ=255)
         gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                            >  1:30701170/1‑68 (MQ=255)
         gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                            >  1:32696626/1‑68 (MQ=255)
         gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                                            >  1:3708005/1‑68 (MQ=255)
          tGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTa                                                           >  1:3862680/1‑68 (MQ=255)
           gACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaa                                                          >  1:19621949/1‑68 (MQ=255)
            aCCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaa                                                          >  1:8729071/1‑67 (MQ=255)
            aCCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCAGTaa                                                          >  1:5820646/1‑67 (MQ=255)
             cccccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaaa                                                         <  1:27849462/67‑1 (MQ=255)
             cccccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAAc                                                        >  1:25489408/1‑68 (MQ=255)
              ccccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTTCGTCGGGAGGGGCTAATTACCGGGAATCa                                                       >  1:12099810/1‑68 (MQ=25)
               cccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAActg                                                      <  1:6066273/68‑3 (MQ=255)
               cccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAg                                                      >  1:14222165/1‑68 (MQ=255)
                    cgtcgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTcc                                                 >  1:18458010/1‑68 (MQ=255)
                        gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                             <  1:27627530/68‑1 (MQ=255)
                        gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                             <  1:16016031/68‑1 (MQ=255)
                        gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                             <  1:28535901/68‑1 (MQ=255)
                        gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                                             <  1:23328282/68‑1 (MQ=255)
                               tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                                        >  1:1071693/1‑66 (MQ=255)
                                 cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                                     >  1:10054902/1‑67 (MQ=255)
                                  tatgCATATGCTGCGCCTACGGCGGGAGGTGCAAATTACCGGTAACCAGGTTCCGGAAATTATCCTGc                                   <  1:9374696/65‑1 (MQ=21)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:21744938/68‑1 (MQ=255)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:25154990/68‑1 (MQ=255)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:20440319/68‑1 (MQ=255)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:29947137/68‑1 (MQ=255)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:31701875/68‑1 (MQ=255)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:33318406/68‑1 (MQ=255)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:1289186/68‑1 (MQ=255)
                                  tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                                   <  1:10464644/68‑1 (MQ=255)
                                   aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                                   <  1:33750752/64‑1 (MQ=255)
                                   aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                                   <  1:20230958/64‑1 (MQ=255)
                                   aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                                  >  1:34094856/1‑68 (MQ=255)
                                   aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                                  >  1:23774747/1‑68 (MQ=255)
                                     gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:12625600/1‑68 (MQ=255)
                                     gCATATGCTGCGCCTACGTCGGGAGGGGCAAAATACCGCTAAACAGCTTCCTGAAATTATCCTGCTTa                                >  1:19129264/1‑68 (MQ=25)
                                     acATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTa                                >  1:9748766/2‑68 (MQ=255)
                                      cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                               >  1:15817011/1‑68 (MQ=255)
                                      cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                               >  1:1513669/1‑68 (MQ=255)
                                      cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa                               >  1:11259431/1‑68 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:26372856/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:1465330/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:18252402/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:34372039/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:2701474/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:26809866/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:6982336/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:7420498/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:10982897/1‑67 (MQ=255)
                                      cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGCTTCCGGAAATTATCCTGCTTa                                >  1:4745800/1‑67 (MQ=255)
                                       atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa                                >  1:22893261/1‑66 (MQ=255)
                                       atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                              <  1:13354688/68‑1 (MQ=255)
                                       atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc                              <  1:15558156/68‑1 (MQ=255)
                                        tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct                             <  1:3553306/68‑1 (MQ=255)
                                          tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                            >  1:4253471/1‑67 (MQ=255)
                                          tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                            >  1:26156823/1‑67 (MQ=255)
                                          tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                            >  1:6627186/1‑67 (MQ=255)
                                          tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                            >  1:7097306/1‑67 (MQ=255)
                                          tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc                            >  1:33420592/1‑67 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGTTAAAAAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:28793012/1‑68 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:22061508/1‑68 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:32010066/1‑68 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:4191224/1‑68 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:17185550/1‑68 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:26030765/1‑68 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:21126739/1‑68 (MQ=255)
                                           gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:29731348/1‑68 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:1990542/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:1380331/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:2740468/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:32374780/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:16344092/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:11760219/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc                          >  1:16503425/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCAGCTTAACtctc                          >  1:5065044/1‑67 (MQ=255)
                                            ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCATGCTTAACtctc                          >  1:17744953/1‑67 (MQ=255)
                                             tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCa                         <  1:5657826/67‑1 (MQ=255)
                                             tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCa                         <  1:30365560/67‑1 (MQ=255)
                                             tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCAc                        >  1:21516314/1‑68 (MQ=255)
                                              gcgcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACg                       <  1:26476535/68‑1 (MQ=255)
                                                gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                     >  1:30980546/1‑68 (MQ=255)
                                                gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                     >  1:12414456/1‑68 (MQ=255)
                                                gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt                     >  1:19370414/1‑68 (MQ=255)
                                                 ccTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg                    >  1:22444155/1‑68 (MQ=255)
                                                 ccTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg                    >  1:14456052/1‑68 (MQ=255)
                                                   tACTTCGGGAGTGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                  <  1:1162213/68‑1 (MQ=255)
                                                   tACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGc                  <  1:2407107/68‑1 (MQ=255)
                                                    aCGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCa                 <  1:7734412/68‑1 (MQ=255)
                                                        cGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAg             <  1:32981577/68‑1 (MQ=255)
                                                        cGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAg             <  1:18932460/68‑1 (MQ=255)
                                                         gggTGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt            <  1:24763238/68‑1 (MQ=255)
                                                         gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt            <  1:5247479/68‑1 (MQ=255)
                                                         gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt            <  1:2940509/68‑1 (MQ=255)
                                                         gggAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGt            <  1:33571526/68‑1 (MQ=255)
                                                           gAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTc          >  1:29162648/1‑68 (MQ=255)
                                                           gAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTc          >  1:16617579/1‑68 (MQ=255)
                                                               ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGt        <  1:24401234/66‑1 (MQ=255)
                                                               ggCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTa       <  1:443155/67‑1 (MQ=255)
                                                                  aaaTTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAg   <  1:30850869/68‑1 (MQ=255)
                                                                   |                                                                   
CACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACCAGTTCGTACCAGA  >  CP009273/2762232‑2762366

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: ‑