Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,589,223 A→G 7.6% V753V (GTT→GTC USA300HOU_1459 ← hypothetical bacteriophage protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,589,2230AG 7.6% 140.9 / 3.8 53V753V (GTT→GTCUSA300HOU_1459hypothetical bacteriophage protein
Reads supporting (aligned to +/- strand):  ref base A (39/10);  new base G (2/2);  total (41/12)
Fisher's exact test for biased strand distribution p-value = 2.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.89e-01

ATAATCTTTTCCAAATCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGGTGTGTT  >  CP000730/1589085‑1589363
                                                                                                                                          |                                                                                                                                              
aTAATCTTTTCCAAATCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTcaac                                                                                                                                              <  2:221012/141‑1 (MQ=255)
              aTCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCAATAGATCCTCTACTATCTCCCTTATCTTTACCAAACCATTCAACAAACACTTCacacc                                                                                                                                >  2:620846/1‑137 (MQ=255)
                   aTTTTCCCACTTTTATTACCATCATATACAGCCCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCGCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAg                                                                                                                           <  2:66299/141‑1 (MQ=255)
                      ttCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGAcc                                                                                                                        >  1:937502/1‑141 (MQ=255)
                           aCTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTAtt                                                                                                                   >  2:913130/1‑141 (MQ=255)
                           aCTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTAtt                                                                                                                   >  2:245245/1‑141 (MQ=255)
                                  ttaCCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCa                                                                                                            >  1:283684/1‑141 (MQ=255)
                                  ttaCCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCa                                                                                                            >  2:593624/1‑141 (MQ=255)
                                  ttaCCATCATATACAAACCCAATTTCTAATTGTCTTAAGATGTTGGAAACCTTTCTAATTTCCATAGAACCTCTACGATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCa                                                                                                            >  2:593671/1‑141 (MQ=255)
                                      ctttttatgCAGACCAATTGTCTAATTTTCTTAGGATGTTTGAAGTCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCATAACATTCAACAAACACTTCCAGCGCACCCACCTTATTTCTTTTAACgg                                                                                                        <  2:157064/136‑2 (MQ=255)
                                          atatACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAACGCACAGCCCTTATTTCTTTCAACGTAATc                                                                                                    >  1:28726/1‑141 (MQ=255)
                                           tataCAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCt                                                                                                   <  2:248430/141‑1 (MQ=255)
                                             taCAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTAc                                                                                                 >  1:644850/1‑141 (MQ=255)
                                                aGACCCATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCCCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACAtt                                                                                             <  1:398574/141‑1 (MQ=255)
                                                   ccaatgtgctaagtgtctTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTACCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTcc                                                                                          <  2:898494/133‑1 (MQ=255)
                                                     aattgtctaattgtctTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTg                                                                                        <  1:514682/141‑1 (MQ=255)
                                                      attgtctaattgtctTAAGACGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTGCTTTCAACGTAATCTACATTTCCTGt                                                                                       >  1:572975/1‑141 (MQ=255)
                                                        tttctaatggtctTAAAATGTTTGAAATCTTTCTGATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACAGTTCACGAGAAACTGGATTAGTTCTTTCAACGTACTCTACATTTCCTGtat                                                                                     >  2:661574/3‑139 (MQ=255)
                                                         gtctaattgtctTAAGTTGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTAGCTCCCTTATCTTTACGAAAACATTCAACAAACACTTCAGGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTgg                                                                                    >  1:467876/1‑141 (MQ=255)
                                                         gtctaattgtctTAAGCTGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTgg                                                                                    >  1:561023/1‑141 (MQ=255)
                                                           ctaattgtctTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCACCGTCATCTACATTTCCTTTTGGTa                                                                                  >  1:120603/1‑141 (MQ=255)
                                                                    ttAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTCCATTTCCTGTCGGTAACATATCac                                                                         >  2:29615/1‑140 (MQ=255)
                                                                    ttAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCaa                                                                         >  2:29645/1‑141 (MQ=255)
                                                                     tAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAAc                                                                        >  1:248897/1‑141 (MQ=255)
                                                                       aGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACAATTCAACaa                                                                      >  2:315094/1‑140 (MQ=255)
                                                                          tGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCAc                                                                   >  2:268104/1‑141 (MQ=255)
                                                                               gAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTgt                                                              >  1:249726/1‑140 (MQ=255)
                                                                                     tttCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACACCACCTTGATAAAAt                                                        >  1:142510/1‑141 (MQ=255)
                                                                                        cTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGt                                                    >  1:190771/1‑141 (MQ=255)
                                                                                         tAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTc                                                   >  1:733495/1‑141 (MQ=255)
                                                                                               ccATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGtt                                             >  1:734679/1‑141 (MQ=255)
                                                                                                   aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCaaa                                         <  1:913130/141‑1 (MQ=255)
                                                                                                   aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCGACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCaaa                                         <  1:245245/141‑1 (MQ=255)
                                                                                                   aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCaaa                                         >  1:393639/1‑141 (MQ=255)
                                                                                                   aGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAAAATCCCGTCAGTAAAATCGTCTTCGttataa                                         >  1:401087/1‑137 (MQ=255)
                                                                                                    gATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAg                                        >  1:131676/1‑141 (MQ=255)
                                                                                                           tactaTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTa                                 >  2:814176/1‑141 (MQ=255)
                                                                                                             ctaTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAg                               >  1:374774/1‑141 (MQ=255)
                                                                                                             ctaTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAg                               >  1:738960/1‑141 (MQ=255)
                                                                                                              taTCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGt                              >  1:143302/1‑141 (MQ=255)
                                                                                                                 ctcCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATAATAACCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCAt                           >  1:880814/1‑141 (MQ=255)
                                                                                                                  tcCCTTATCTGTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTGGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCATAGATAGTTAAGTCATc                          >  2:319999/1‑141 (MQ=255)
                                                                                                                   cccTTATCTTTACCAGAACATTCAACGAACACTTTAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGTTAACATATCAACATCACCTTGATAAAATCGTCTTCGTCCAAAGATAGTTAAGTCATcc                         <  1:571909/141‑1 (MQ=255)
                                                                                                                   cccTTATCTTTACCAAAACATTCAACAAACACTTCCAGCACACAGCCCTTATTTCTTTCAACGTACACTTAATCTTCCTTTCATGACATCTCAACATTGCCATGTAAAATGCGTCTTCGTTCAAAGATAGTTAAGTCATcc                         >  2:452596/1‑141 (MQ=255)
                                                                                                                   cccTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATcc                         <  2:795851/141‑1 (MQ=255)
                                                                                                                      ttATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCGACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCaa                      >  1:512509/1‑141 (MQ=255)
                                                                                                                       tATCTTTACCAAAACATTCAACAAACACTTCAAGCGCAAAGACCTTATTTCTTTCCACGTAATCTACATTTCCTGTTGGTAACCTATAAACATCCCTTTCATATAAATTTACTCGTTCAGAGGGAGTCAAGTCATCCCCAt                     >  2:890358/1‑141 (MQ=255)
                                                                                                                         tCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTGCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACAGCACCTTTATAAAAGCGTCTTCGTTCAAGGATAGTTAAGTAATCCCAATTg                   >  1:38793/1‑141 (MQ=255)
                                                                                                                           tttACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCt                 >  2:588974/1‑141 (MQ=255)
                                                                                                                              aCCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAgg              <  2:733495/141‑1 (MQ=255)
                                                                                                                              aCCAAAACATTCAACAAACACTTCAAGCGCACACACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGACAGTTAAGTCATCCCAATTGCTAgg              <  1:604109/141‑1 (MQ=255)
                                                                                                                                 aaaaCATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAAATAGTTAAGTCATCCCAATTGACAGGAAt           >  2:347842/1‑141 (MQ=255)
                                                                                                                                  aaaCATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAAtt          >  2:490100/1‑141 (MQ=255)
                                                                                                                                        tCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATACCCTTGCTAAAATCGTCTGCGTTCAAAGACAGTTAAGTAATCCCAATGGCTGGGATTAGgtgtg    >  2:803617/1‑141 (MQ=255)
                                                                                                                                         caaaaaACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGgtgtgt   >  2:299830/1‑141 (MQ=255)
                                                                                                                                          aacaaacaCTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGGTGTGtt  >  2:893448/1‑141 (MQ=255)
                                                                                                                                          aacaaacaCTTCAAGAACACAGACCTCTGTTCTTTCAACGTAATCTACATTTCCTGCCGGTCACATATCAACATCACCTTGGACAAATGACCTTCGTCCAACGAAAGTACAGTCATCCAACTGGCTAGGAATTgacgagag  >  2:913752/1‑134 (MQ=255)
                                                                                                                                          |                                                                                                                                              
ATAATCTTTTCCAAATCGAATTTTCCCACTTTTATTACCATCATATACAGACCAATTGTCTAATTGTCTTAAGATGTTTGAAATCTTTCTAATTTCCATAGATCCTCTACTATCTCCCTTATCTTTACCAAAACATTCAACAAACACTTCAAGCGCACAGACCTTATTTCTTTCAACGTAATCTACATTTCCTGTTGGTAACATATCAACATCACCTTGATAAAATCGTCTTCGTTCAAAGATAGTTAAGTCATCCCAATTGCTAGGAATTGGTGTGTT  >  CP000730/1589085‑1589363

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: