Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,119,406 T→C 7.3% K280K (AAA→AAG)  USA300HOU_1992 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,119,4060TC 7.3% 150.8 / 3.4 55K280K (AAA→AAG) USA300HOU_1992hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (31/20);  new base C (2/2);  total (33/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

TCATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTAC  >  CP000730/2119272‑2119546
                                                                                                                                      |                                                                                                                                            
tcATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAAt                                                                                                                                        >  1:454619/1‑141 (MQ=255)
 cATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAAtt                                                                                                                                       <  2:432227/141‑1 (MQ=255)
     cGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGa                                                                                                                                   <  1:58910/141‑1 (MQ=255)
     cGTGATTTGTTGTTAGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGACTTCTATACGTTTCAATTCTgt                                                                                                                                   >  2:431024/1‑140 (MQ=255)
        gATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTg                                                                                                                                <  1:400361/141‑1 (MQ=255)
         aTTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGt                                                                                                                               <  2:92287/141‑1 (MQ=255)
          tttGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGtt                                                                                                                              >  1:137618/1‑141 (MQ=255)
          tttGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGtt                                                                                                                              >  1:137635/1‑141 (MQ=255)
                gtttgtttTGCTTTAATCTTGTTTTAAGATTCGCAACCGTTCCATTTTCAACGTGTAGCTCATTTGTTAAAGCATGTATTTTGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAg                                                                                                                        <  2:290880/141‑1 (MQ=255)
                  ttgtttTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTTTTTTGTTAAAGCATGGCTTTTGTTCTCATTGCTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGCTTGTTTATCAGCt                                                                                                                      <  2:75748/141‑1 (MQ=255)
                   tgtttTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTa                                                                                                                     <  1:158869/141‑1 (MQ=255)
                          cTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGAtt                                                                                                              >  1:326868/1‑141 (MQ=255)
                             tAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACg                                                                                                           <  1:240729/141‑1 (MQ=255)
                               aTCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTa                                                                                                         <  2:283525/141‑1 (MQ=255)
                                  tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                                      >  1:217075/1‑141 (MQ=255)
                                  tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                                      <  2:168315/141‑1 (MQ=255)
                                  tcGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGCAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaat                                                                                                      >  2:199650/1‑141 (MQ=255)
                                   cGTTTTAAGGTTTGCTACTGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatt                                                                                                     >  1:451228/1‑141 (MQ=255)
                                   cGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatt                                                                                                     >  1:150850/1‑141 (MQ=255)
                                    gTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatta                                                                                                    >  2:41402/1‑141 (MQ=255)
                                    gTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAaatta                                                                                                    >  1:165682/1‑141 (MQ=255)
                                    gTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACATAaatta                                                                                                    >  1:132580/1‑141 (MQ=255)
                                         aaGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATttc                                                                                               >  1:428174/1‑141 (MQ=255)
                                           ggTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATttctt                                                                                             <  1:193813/141‑1 (MQ=255)
                                             tttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTcc                                                                                           <  2:415041/141‑1 (MQ=255)
                                              ttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGTGCTGTTATTGTCTTCTATGCGTTTCAATTTTGATTGTTTATCAGCTAATTGATTACGCAAATTATTttctttct                                                                                          >  2:416462/1‑141 (MQ=255)
                                              ttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCt                                                                                          <  1:32422/141‑1 (MQ=255)
                                              ttGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCt                                                                                          <  1:221029/141‑1 (MQ=255)
                                                        tCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGTATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTg                                                                                <  2:413712/141‑1 (MQ=255)
                                                                   cgtgtagctCATTTGTTAAAGCATGTATTTTGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAGCTAATTGGTTACGCAAATTAATTTCTTCTGCACCGTTTTGAATATCTATAc                                                                     >  1:393940/9‑141 (MQ=255)
                                                                   cgtgtagctCATTTGTTAAAGCATGTATTTTGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAGCTAATTGGTTACGCAAATTAATTTCTTCTGCACCGTTTTGAATATCTATAc                                                                     >  1:393923/9‑141 (MQ=255)
                                                                   cGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATAc                                                                     >  2:39838/1‑141 (MQ=255)
                                                                    gtgtAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTAAAGTTGTGGATATCTATACg                                                                    >  1:251078/1‑141 (MQ=255)
                                                                      gtAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTCACGTGTTGTATATCTATACGCt                                                                  <  2:90742/141‑1 (MQ=255)
                                                                      gtAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCt                                                                  <  1:378988/141‑1 (MQ=255)
                                                                             aTTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTTAATATCTTTACTCTCAttttt                                                           >  2:413136/1‑140 (MQ=255)
                                                                                tGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAg                                                        >  1:366388/1‑141 (MQ=255)
                                                                                     aaGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCt                                                   >  1:12601/1‑141 (MQ=255)
                                                                                     aaGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCt                                                   <  2:72973/141‑1 (MQ=255)
                                                                                       gCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCa                                                 <  2:74471/141‑1 (MQ=255)
                                                                                                ttGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAGCTAATTGGTTACGCAAATTAATTTCTTCTGCACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGt                                        <  1:333051/141‑1 (MQ=255)
                                                                                                 tGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGtt                                       >  2:404706/1‑141 (MQ=255)
                                                                                                  gTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGttt                                      >  1:161364/1‑141 (MQ=255)
                                                                                                   ttCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTg                                     >  1:328048/1‑141 (MQ=255)
                                                                                                       cATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATaa                                 >  1:388936/1‑141 (MQ=255)
                                                                                                           aCTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGc                             >  1:334456/1‑141 (MQ=255)
                                                                                                                 gcTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGtatct                       >  2:367865/1‑141 (MQ=255)
                                                                                                                     ttATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCa                   >  2:431108/1‑141 (MQ=255)
                                                                                                                      tATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCAt                  >  2:190090/1‑141 (MQ=255)
                                                                                                                         tGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTAt               <  1:230739/141‑1 (MQ=255)
                                                                                                                         tGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTAt               <  1:59772/141‑1 (MQ=255)
                                                                                                                          gTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATc              >  1:204850/1‑141 (MQ=255)
                                                                                                                               ctATGCGTTTCAATTCTGATTGTTTATCAACTAATTGGTTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACACTCATTTTCATGTTGCGCAATTTCTTGTTTGATAATTTAGTAGCTATCGTTATCGTAtt         >  2:107066/1‑141 (MQ=255)
                                                                                                                                tATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTc        >  1:389059/1‑141 (MQ=255)
                                                                                                                                tATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTc        >  2:58130/1‑141 (MQ=255)
                                                                                                                                      tttCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTAc  >  1:15831/1‑141 (MQ=255)
                                                                                                                                      |                                                                                                                                            
TCATGCGTGATTTGTTGTTTGTTTTGCTTTAATCTCGTTTTAAGGTTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTAC  >  CP000730/2119272‑2119546

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