Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,119,459 T→C 9.2% K263E (AAG→GAG) ‡ USA300HOU_1992 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,119,4590TC 9.2% 139.9 / 4.9 54K263E (AAG→GAG) ‡USA300HOU_1992hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (31/18);  new base C (2/3);  total (33/21)
Fisher's exact test for biased strand distribution p-value = 3.66e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

TCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAATATCTTT  >  CP000730/2119328‑2119594
                                                                                                                                   |                                                                                                                                       
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)
                                                                              cttCCATTCTGATTGTTTATCAGCTCATTGGTTACGCAAATTATTTTCTTCCGCACCCATCTGAATATCTATACGCTAACTTTCTCGTTGCTCAATTTCTTGTTTTATGATTGTGTGTCTATCATTATCGAATTCCGGTAc                                                  <  1:269986/140‑1 (MQ=255)
                                                                                 cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                               >  1:48436/1‑141 (MQ=255)
                                                                                 cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                               <  1:321196/141‑1 (MQ=255)
                                                                                 cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                               >  2:199908/1‑141 (MQ=255)
                                                                                 cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTCCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                               <  1:372627/141‑1 (MQ=255)
                                                                                      cTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCt                                          <  2:117313/141‑1 (MQ=255)
                                                                                       tGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCtt                                         <  1:453720/141‑1 (MQ=255)
                                                                                        taTTGTTTATCAGCTAATTGATTTCGTAAATTATTTTCTTTCTTACTTTTTTGAATATCTATACGGTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCTTTATCGAATTCTGTTACATCCTGCTTa                                        <  2:333773/140‑1 (MQ=255)
                                                                                         aTTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTTCCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAt                                       <  1:221610/141‑1 (MQ=255)
                                                                                           tGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAttt                                     <  1:274684/141‑1 (MQ=255)
                                                                                            gTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCACTTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAtttt                                    >  1:233748/1‑141 (MQ=255)
                                                                                            gTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTAtttt                                    >  2:383532/1‑141 (MQ=255)
                                                                                               tATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTttgtt                                 >  2:220968/1‑141 (MQ=255)
                                                                                                aTCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTttgttg                                >  1:174948/1‑141 (MQ=255)
                                                                                                   aGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTgtgt                             <  1:348084/141‑1 (MQ=255)
                                                                                                        aTTGATTACGTAAATTAATTTCTTCCTTACTGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCATGCTTATTTTGTTGTGTTTGGt                        >  1:255567/1‑141 (MQ=255)
                                                                                                               aCGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACg                 >  2:168201/1‑141 (MQ=255)
                                                                                                                  tAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTAt              >  2:450912/1‑141 (MQ=255)
                                                                                                                    aattaattTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCg            <  2:52708/141‑1 (MQ=255)
                                                                                                                     attaattTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCgg           >  2:333699/1‑141 (MQ=255)
                                                                                                                        aattTCTTCTGCACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTTATGATTGTGTGTCTATCATTATCGAATTCCGGTACATCCTGCTTATTTTGTTGCGTTTGGTTAATACGTATCGGAat        <  2:263818/141‑1 (MQ=255)
                                                                                                                         attTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAata       >  2:149964/1‑141 (MQ=255)
                                                                                                                          tttCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAatat      >  2:396355/1‑141 (MQ=255)
                                                                                                                          tttCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGGTGCTCAATTTCTTGTTTGATAATTGCGTAGCTATCAGTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGGTTGGTGAATACGTATCGGAatat      >  2:156429/1‑141 (MQ=255)
                                                                                                                              ttcCTTACCGTTTTGAATATCTATACTCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAatatcttt  <  2:454619/141‑1 (MQ=255)
                                                                                                                              ttcCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAatatcttt  <  2:185373/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                       
TCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAATATCTTT  >  CP000730/2119328‑2119594

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑