Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,762,281 C→T 6.9% R86R (CGC→CGT)  yfjQ → CP4‑57 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,762,2810CT 6.9% 1730.2 / 85.7 534R86R (CGC→CGT) yfjQCP4‑57 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (333/163);  new base T (24/13);  total (357/177)
Fisher's exact test for biased strand distribution p-value = 8.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.69e-01

Only 100 of 553 total aligned reads displayed.

CATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATG  >  CP009273/2762214‑2762348
                                                                   |                                                                   
   tCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTa                                                                  <  1:5124325/68‑1 (MQ=255)
   tCTTTGCCTGGCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTa                                                                  <  1:6193957/68‑1 (MQ=255)
    cTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTAc                                                                 <  1:10032809/68‑1 (MQ=255)
    cTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTAc                                                                 <  1:21752067/68‑1 (MQ=255)
    cTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTAc                                                                 <  1:12091913/68‑1 (MQ=255)
     tttGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACg                                                                <  1:20296532/68‑1 (MQ=255)
      ttGCCTGTCAGACAGGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGt                                                               <  1:31007111/68‑1 (MQ=255)
                  cacGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAgggg                                                      <  1:24230645/65‑1 (MQ=255)
                  cacGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAgggg                                                      <  1:12510921/65‑1 (MQ=255)
                  cacGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaa                                                   >  1:32105872/1‑68 (MQ=255)
                   acGGGTACGTGCCCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                  >  1:19331344/1‑68 (MQ=255)
                   acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                  <  1:21146970/68‑1 (MQ=255)
                   acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                  >  1:3822194/1‑68 (MQ=255)
                   acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                  >  1:4353539/1‑68 (MQ=255)
                   acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                  >  1:4666792/1‑68 (MQ=255)
                   acGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCaaa                                                  >  1:10889687/1‑68 (MQ=255)
                           gTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGt                                          >  1:30701170/1‑68 (MQ=255)
                            tGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTa                                         >  1:28249535/1‑68 (MQ=255)
                             gACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCTATTTACCGGTaa                                        >  1:22779043/1‑68 (MQ=255)
                             gACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTaa                                        >  1:15814762/1‑68 (MQ=255)
                               cccccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAAc                                      >  1:24841439/1‑68 (MQ=255)
                                  ccGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAgg                                   <  1:28579574/68‑1 (MQ=255)
                                   cgtcgtcgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGt                                  <  1:1506533/68‑1 (MQ=255)
                                      cgtcgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTcc                               >  1:5726496/1‑68 (MQ=255)
                                         cgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGa                            >  1:26104866/1‑68 (MQ=255)
                                         cgtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGa                            >  1:19081080/1‑68 (MQ=255)
                                          gtGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaa                           <  1:16016031/68‑1 (MQ=255)
                                           tGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGaaa                          >  1:23328500/1‑68 (MQ=255)
                                            gAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAAt                         <  1:11386292/68‑1 (MQ=255)
                                              gCATACTAAGCATATTCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAAtt                        <  1:19576734/67‑1 (MQ=255)
                                              gCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAAtt                        <  1:12892075/67‑1 (MQ=255)
                                              gCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTa                       >  1:34338447/1‑68 (MQ=255)
                                                 tACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTAt                      >  1:31835362/1‑66 (MQ=255)
                                                  aCTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCt                   <  1:3253376/68‑1 (MQ=255)
                                                   cTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACAGGTAAACAGGTTCCGGAAATTATACTg                  >  1:29482162/1‑68 (MQ=255)
                                                    tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTATACAGGTTCCGGAAATTATCCTGc                 <  1:5884287/68‑1 (MQ=255)
                                                    tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                 <  1:33318406/68‑1 (MQ=255)
                                                    tAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGc                 <  1:10464644/68‑1 (MQ=255)
                                                    tAAGCATATGCTGCGCCTACGGCGGGAGGGGCAAATTACCGGTAAACAGGTTTCGGAAATTATCCTGc                 <  1:33665442/68‑1 (MQ=21)
                                                     aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                 <  1:40736/64‑1 (MQ=255)
                                                     aaacATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGc                 <  1:17195611/64‑1 (MQ=255)
                                                     aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                >  1:8150180/1‑68 (MQ=255)
                                                     aaGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCt                >  1:2651166/1‑68 (MQ=255)
                                                      aGCATATGCTGCGCCTACGTCGGGAAGTGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCtt               >  1:14572712/1‑68 (MQ=255)
                                                       gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:15246836/1‑68 (MQ=255)
                                                       gCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:9493130/1‑68 (MQ=255)
                                                        cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa             <  1:7816833/68‑1 (MQ=255)
                                                        cATATGTTACGTCTTCGCAGGGAAGGGCATATTAACGGGCAGGAAGTTCCTGAAATTATCCTGCTTaa             >  1:423791/1‑68 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:27495277/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:29881722/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:13167253/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:4916929/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:11653901/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:26920337/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:26372856/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:18252402/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:6982336/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:25305116/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:18866903/1‑67 (MQ=255)
                                                        cATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:7420498/1‑67 (MQ=255)
                                                         atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:20387605/1‑66 (MQ=255)
                                                         atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTa              >  1:24655138/1‑66 (MQ=255)
                                                         atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc            <  1:15596844/68‑1 (MQ=255)
                                                         atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc            <  1:13354688/68‑1 (MQ=255)
                                                         atatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAc            <  1:30271242/68‑1 (MQ=255)
                                                          tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct           <  1:27994078/68‑1 (MQ=255)
                                                          tatGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAAct           <  1:3553306/68‑1 (MQ=255)
                                                           atGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc          <  1:32811250/68‑1 (MQ=255)
                                                            tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc          >  1:9818991/1‑67 (MQ=255)
                                                            tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc          >  1:7097306/1‑67 (MQ=255)
                                                            tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc          >  1:20950094/1‑67 (MQ=255)
                                                            tgctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAActc          >  1:6627186/1‑67 (MQ=255)
                                                            tgctgcGCCTACGTCGGGAGGGCCAAATTACCGGAAAACAGGTTCCGGAAAATATCCTGCTTAActct         >  1:11824256/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGTTAAAAAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:28793012/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:18406827/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:9141308/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:22061508/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:29185305/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:16540241/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:29731348/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:33818588/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:30858016/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:3341311/1‑68 (MQ=255)
                                                             gctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:14265670/1‑68 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTTACtctc        >  1:3642915/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:1990542/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:25940813/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:11162926/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:23905936/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:12308943/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:12707709/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:16503425/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:1380331/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACtctc        >  1:16344092/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCATGCTTAACtctc        >  1:17744953/1‑67 (MQ=255)
                                                              ctgcGCCTACGTCGGCAGGCGCTAAATACCGGTAATCAGGTTCCGGAATTTATCCTGCTTAACtctc        >  1:27226229/1‑67 (MQ=255)
                                                               tgcGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCa       <  1:31616790/67‑1 (MQ=255)
                                                                  gcCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGAt   >  1:27742712/1‑68 (MQ=255)
                                                                   ccTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg  >  1:22444155/1‑68 (MQ=255)
                                                                   ccTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATg  >  1:21598623/1‑68 (MQ=255)
                                                                   |                                                                   
CATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATG  >  CP009273/2762214‑2762348

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: ‑