Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,560,985 C→A 17.4% intergenic (+87/‑383) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,560,9850CA17.4% 109.8 / 2.8 51intergenic (+87/‑383)yffL/yffMCPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (22/19);  new base A (4/6);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 4.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATCGGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAG  >  NC_000913/2560837‑2561129
                                                                                                                                                    |                                                                                                                                                
gATCGGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTc                                                                                                                                                  <  4:18315/149‑1 (MQ=255)
       aGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTTGGTCAAAAGTTGCCGTTAAAGGAGGGTCaaattat                                                                                                                                           >  6:88498/1‑145 (MQ=255)
       aGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGTTGGGTCAAAAGtt                                                                                                                                           >  7:353272/1‑149 (MQ=255)
       aGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGtt                                                                                                                                           >  2:257318/1‑149 (MQ=255)
         aaaGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGACAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGc                                                                                                                                         <  4:139473/149‑1 (MQ=255)
               aGTGCAACGAATACCAGTTATTATTCTAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTTCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCAGTTAGTGGTGGGGCAAAAGTTGCCGTTaa                                                                                                                                   <  1:410038/149‑1 (MQ=255)
                gTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAg                                                                                                                                  <  5:359645/149‑1 (MQ=255)
                 tGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAATGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAgg                                                                                                                                 <  3:378497/149‑1 (MQ=255)
                    aaCGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTgg                                                                                                                              <  1:56990/149‑1 (MQ=255)
                          tACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGCTGGGTAAAAAGTTGCCGTTTAGCTGGGACaaa                                                                                                                        >  3:301623/1‑149 (MQ=255)
                             cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCATAAGTTGCCGTTTAGGTGGGTCaaaatt                                                                                                                     >  5:159132/1‑147 (MQ=255)
                             cAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGACTTTTCTTTGGCTTAATTACATGAATTAAGGTGGGTCAAAAGTTGACGTTAGTGGTGGGTCAAAATTGGCCGTTAAGGTTGGTaaaattt                                                                                                                     >  5:297017/1‑146 (MQ=255)
                              aGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGtt                                                                                                                    >  4:241817/1‑149 (MQ=255)
                               gTTATTATTCAAGCCGTACAACATGAAAAAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCaaaa                                                                                                                                              <  2:214449/122‑1 (MQ=255)
                                ttattaTTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTg                                                                                                                   <  6:318702/148‑1 (MQ=255)
                                  attattCAAGCCGTACAACATGAAATAACGGCATCAGGCGGGCAATGTTACTGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGAAGCCGTTAGTGGTGGGGAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGcc                                                                                                                 <  1:113792/148‑1 (MQ=255)
                                   ttattCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCATAAGTTGCCTTTTAGGGGGGTCAAAAGTTGACGt                                                                                                               >  3:70754/1‑149 (MQ=255)
                                   ttattCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCg                                                                                                                <  8:359346/148‑1 (MQ=255)
                                    tattCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCCGt                                                                                                               >  5:132182/1‑148 (MQ=255)
                                     attCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTAAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGtg                                                                                                              >  3:227868/1‑147 (MQ=255)
                                      ttCAAGCCGTACAACATGAAATAACGGAATCCGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCGTTaa                                                                                                            <  7:328566/149‑1 (MQ=255)
                                      ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTTGTGGTGGGTCAAATGTAGCAGTTAAGGAGGGTCCAAAGTTGCCGtt                                                                                                              >  3:369251/1‑147 (MQ=255)
                                      ttCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTaa                                                                                                            <  8:146675/149‑1 (MQ=255)
                                         aaGCCGTACAACATGAAATAACGTAATAAGGCTGTCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGGCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGGCAAAAGTTGCCGTTAAGGt                                                                                                         <  6:244370/149‑1 (MQ=255)
                                         aaGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTTGGTAAAAATTTGCGGTTAAGGTGGGACATAAGATGACgcttag                                                                                                           >  3:345379/1‑142 (MQ=255)
                                         aaGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTTAGGt                                                                                                         >  7:73849/1‑149 (MQ=255)
                                         aaGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGt                                                                                                         <  1:358983/149‑1 (MQ=255)
                                         aaGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGt                                                                                                         <  3:241817/149‑1 (MQ=255)
                                         aaGCCGTACAACATGAAATAACGGAATCAGGCGCGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGt                                                                                                         <  3:330285/149‑1 (MQ=255)
                                               tACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAATGGAGGGTAAAATTTTGCCTTAAAGGGGGCTCAAAAGTTGAAGTAAaggaggatg                                                                                                    >  8:219948/1‑145 (MQ=255)
                                                 caacaTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTGAGTGGTGGGTCATATGTTGCCTTTTAGGAGGGTCAAGAGTTGACGGTAAGGTGGGtgtc                                                                                                  >  5:213160/1‑145 (MQ=255)
                                                    caTGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAATTTGCCGTTAAGGTGGGGGAAAAGt                                                                                              >  7:364078/1‑149 (MQ=255)
                                                                         gggCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTATTGGTGGGTCAAAAGTTGACTTGAAGGTGTGGGAAAATTTTCAGTTTACGTGGGTGAAAATTTGACGAGAAAGAATTct                                                                             >  8:78073/1‑145 (MQ=255)
                                                                                         ttttCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGACGAGTAAGAATTCTACTATTAATAATTCTAGGCg                                                         >  3:269973/1‑149 (MQ=255)
                                                                                                       aatCCATGAATTCAGGCGGGCCAAACGCCGCCGTTAGTGGTGGGTCAAAACCAGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTa                                           <  1:287857/147‑1 (MQ=37)
                                                                                                       aTTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGtttttt                                            <  7:63356/148‑1 (MQ=255)
                                                                                                         ttaaTGAATTCAGCCTGGTAAAAAGTTGCCGTTCCGGGGGGGTAATATGTTGCCTTATCGTTGGGTCAAAAGTTGCCTTTCAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGc                                         <  2:14841/146‑1 (MQ=255)
                                                                                                          ccaagcaTTCTGGCGTGTAAAAATTAGGCGTTAGGGGGGGGTAAAAAGGTGCCTTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGc                                         <  7:219948/142‑1 (MQ=25)
                                                                                                           cATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAATGTTGACGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGACt                                       >  3:106923/1‑149 (MQ=255)
                                                                                                                    aGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCcggtcgg                              <  3:269228/149‑1 (MQ=255)
                                                                                                                       ggggTAAAAAGCAGCCCTTATTGTTGGCTAAAAAGTTGCCTTTAAGGTGGGTCAAAAGGTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCa                           <  1:257318/148‑1 (MQ=37)
                                                                                                                        gggTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCa                           >  7:89636/1‑148 (MQ=255)
                                                                                                                                   tggccttATTGGGGGGTAAATTGGTGCCTTTTCGGTGGGTCAATTGTTGCCTTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGc                <  8:33787/143‑1 (MQ=255)
                                                                                                                                    gCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc               >  5:196051/1‑148 (MQ=255)
                                                                                                                                      cGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGcc               >  1:37139/1‑146 (MQ=255)
                                                                                                                                       gTTTGTGGTGGTTAAAAAGTCGCCGTTTAGTTGGGTCAAAAGTTGGCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAAATCTACTATTAAGAATTCTAGGCCACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTaga           <  7:119654/149‑1 (MQ=38)
                                                                                                                                        ttAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTagag          >  3:273488/1‑149 (MQ=255)
                                                                                                                                            tggtggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTa       >  1:96054/1‑148 (MQ=255)
                                                                                                                                            tggtggGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGACGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCATCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTa       >  6:9971/1‑148 (MQ=255)
                                                                                                                                            gggtggGTCATATGTTGCCTTTTAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTa       <  8:73849/147‑1 (MQ=255)
                                                                                                                                              gtggGTCAAGAGATGCCGTTACCGTGGGTCAAAAGTAGCCTCTATGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAAc    <  5:96086/149‑1 (MQ=255)
                                                                                                                                                   tCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACag  >  7:103824/1‑146 (MQ=255)
                                                                                                                                                    cAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGTCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATaga                       <  3:106040/124‑1 (MQ=255)
                                                                                                                                                    cAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGTCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATaga                       >  4:106040/1‑124 (MQ=255)
                                                                                                                                                    |                                                                                                                                                
GATCGGCAGAAAGGGAGTGCAACGAATACCAGTTATTATTCAAGCCGTACAACATGAAATAACGGAATCAGGCGGGCAATGTTCCCGCCTTTTCTTTGCCTTAATTCCATGAATTCAGGTGGGTCAAAAGTTGCCGTTAGTGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGTTAAGGTGGGTCAAAAGTTGCCGAGTAAGAATTCTACTATTAAGAATTCTAGGCGACGGGAGTTTTTTAGCCTCCCGGTCGGTCATAGAGAGTCGCCTAGAGTTAAACAG  >  NC_000913/2560837‑2561129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑