Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,119,457 C→T 7.1% K263K (AAG→AAA) ‡ USA300HOU_1992 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,119,4570CT 7.1% 153.4 / 2.8 56K263K (AAG→AAA) ‡USA300HOU_1992hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (31/21);  new base T (2/2);  total (33/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.98e-01

TTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAATATCTTT  >  CP000730/2119317‑2119594
                                                                                                                                            |                                                                                                                                         
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                                                                                                                     >  1:393923/9‑141 (MQ=255)
                      cgtgtagctCATTTGTTAAAGCATGTATTTTGTTCTCATTACTGGCGCTATTATTAGCTTCTATGCGCTTCAATTCTGATTGTTTATCAGCTAATTGGTTACGCAAATTAATTTCTTCTGCACCGTTTTGAATATCTATAc                                                                                                                     >  1:393940/9‑141 (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                                                        >  2:58130/1‑141 (MQ=255)
                                                                                   tATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTc                                                        >  1:389059/1‑141 (MQ=255)
                                                                                         tttCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTAc                                                  >  1:15831/1‑141 (MQ=255)
                                                                                         cttCCATTCTGATTGTTTATCAGCTCATTGGTTACGCAAATTATTTTCTTCCGCACCCATCTGAATATCTATACGCTAACTTTCTCGTTGCTCAATTTCTTGTTTTATGATTGTGTGTCTATCATTATCGAATTCCGGTAc                                                  <  1:269986/140‑1 (MQ=255)
                                                                                            cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                               >  2:199908/1‑141 (MQ=255)
                                                                                            cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                               <  1:321196/141‑1 (MQ=255)
                                                                                            cAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATc                                               >  1:48436/1‑141 (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)
                                                                                                                                            |                                                                                                                                         
TTTGCTACCGTTCCATTTTCAACGTGTAATTCATTTGTTAAAGCATGGATTTTGTTCTCATTACTTGCGCTGTTATTGTCTTCTATGCGTTTCAATTCTGATTGTTTATCAGCTAATTGATTACGTAAATTAATTTCTTCCTTACCGTTTTGAATATCTATACGCTCATTTTCAAGTTGCTCAATTTCTTGTTTGATAATTGCGTATCTATCATTATCGAATTCTGGTACATCCTGCTTATTTTGTTGTGTTTGGTTAATACGTATCGGAATATCTTT  >  CP000730/2119317‑2119594

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: ‑