Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,315 G→A 10.5% Y79Y (TAC→TAT)  USA300HOU_0026 ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,3150GA10.5% 132.8 / 5.8 56Y79Y (TAC→TAT) USA300HOU_0026IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base G (24/25);  new base A (3/3);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

TTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATAT  >  CP000730/36175‑36452
                                                                                                                                            |                                                                                                                                         
ttACTAAATTGTTTAACGGTACGTTTGATAATCGCATATGCTTAATGTGTATCTCGTTTCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATg                                                                                                                                           <  2:173622/141‑1 (MQ=11)
       aTTGTTTAATGAGACGATTGATAAACGCATATGCTGAATGATTGTCTCGATGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGGTATAAATAGCTCCATATTCCTTTTATTTTTATGTACGtct                                                                                                                                    >  1:63434/1‑141 (MQ=11)
             tAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCaa                                                                                                                              <  1:391695/141‑1 (MQ=32)
                tGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATAc                                                                                                                           <  1:434330/141‑1 (MQ=32)
                   gagtgttgtgcaaCGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATCTCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATTTACGTCTCATCAATACGcc                                                                                                                        <  1:12044/130‑1 (MQ=11)
                    aCGTTTGATAAACGAATATACTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCTCTTTCCTTTTATTTTGATGTACGTCTCATCAATACACCa                                                                                                                       >  1:301031/1‑141 (MQ=11)
                     cGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCAt                                                                                                                      >  2:54250/1‑141 (MQ=17)
                        ttGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCCTTTg                                                                                                                   >  1:163164/1‑141 (MQ=17)
                           aTAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCATTTTATTTTGATGTACGTCTCATCAATACGCCATTTTtaa                                                                                                                >  2:372056/1‑141 (MQ=17)
                              aaCGGATATGCTGAATGATTATCTCGTGGGTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCGTTTTCCTTTTATTTTTATGTACGTCTCATCAATACGCCATTTGtaataa                                                                                                             <  1:54767/141‑1 (MQ=11)
                                cGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGc                                                                                                           >  1:330927/1‑141 (MQ=35)
                                            aTGATTATCTCGTTGCTTACGCAACCAAATCTCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATGAATACGCCATTTGTAATAAGCTTTTTTATGCtt                                                                                               <  2:304469/141‑1 (MQ=255)
                                                  aTCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttctt                                                                                         >  2:155169/1‑141 (MQ=40)
                                                   tctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTTTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttcttc                                                                                        <  2:438116/141‑1 (MQ=255)
                                                   tctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCTATTTTCCTTTTATTTTGATGTACGTCTCATCAATCCGCCATTTGTACTAAGTTTTTTTATGCTTTttcttc                                                                                        >  1:182092/1‑141 (MQ=255)
                                                   tctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttcttc                                                                                        <  2:438068/141‑1 (MQ=40)
                                                   tctaGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTttcttc                                                                                        <  1:423537/141‑1 (MQ=255)
                                                    ctcGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTGTTTATGCTTTTTCTTcc                                                                                       <  1:223389/141‑1 (MQ=25)
                                                    ctagTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTcc                                                                                       <  1:451024/138‑1 (MQ=255)
                                                          gCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCAACAttt                                                                                 >  2:433556/1‑141 (MQ=255)
                                                           cTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAAtttt                                                                                >  2:453092/1‑140 (MQ=255)
                                                            gtaagCAACCAAATATCTAATGTATGTCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGa                                                                               >  2:181296/5‑141 (MQ=255)
                                                             tACGCAACCAAATCTCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACTTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGAt                                                                              <  1:432081/141‑1 (MQ=255)
                                                             tACGCAACCAAATATCTAATGTATGTCCCTCTTCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGGACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGAt                                                                              <  1:432182/141‑1 (MQ=255)
                                                             tACGCAACCAAATATCCAATGTATGTCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGAt                                                                              <  1:54250/141‑1 (MQ=255)
                                                              aCGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATa                                                                             >  2:168671/1‑141 (MQ=40)
                                                              aCGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGCCACGATATAAATCGATCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATCTGTAATAAGCTCTTTTATGCTTTTTCTTCCAAATTTgcca                                                                             <  2:406855/141‑4 (MQ=11)
                                                               cGCAAACAAACATGCTATGTATGTCCCTCTGCATCCATGGCACGATATAAATCGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTACGCTTTTTCTTCCAAATTTGATAc                                                                            <  2:66623/141‑1 (MQ=14)
                                                                 cAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAATTTGGATACaa                                                                          >  2:359524/1‑141 (MQ=255)
                                                                   aCCAAATATCTAATGGATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATaaaa                                                                        <  2:460494/141‑1 (MQ=255)
                                                                        atatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCGCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTggg                                                                   >  2:152274/1‑141 (MQ=255)
                                                                         tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTgggg                                                                  <  2:348516/141‑1 (MQ=255)
                                                                         tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTgggg                                                                  <  2:413688/141‑1 (MQ=255)
                                                                         tatCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTATTCTTCCAAATTTGATACAACATTgggg                                                                  >  2:33162/1‑141 (MQ=255)
                                                                                   atgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAACATTggggacgatccgtc                                                        >  1:419953/1‑131 (MQ=255)
                                                                                    tgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGa                                                       <  2:387828/141‑1 (MQ=255)
                                                                                    tgtCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGa                                                       <  2:387833/141‑1 (MQ=255)
                                                                                      tCCCTCTTCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACTTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACACAATTTGGGCGTATTTTTGGAc                                                     >  1:45360/1‑141 (MQ=14)
                                                                                      tCCCTCTGTATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCACATTTGGTATCAAATTGTGGAGTATGCTTTAAc                                                     >  1:379607/1‑141 (MQ=11)
                                                                                       cccTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGACTATTCTTTAAcc                                                    >  2:85203/1‑141 (MQ=255)
                                                                                        ccTCTGCATCAATGGCACGATATACATAACTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAAccc                                                   <  2:301031/141‑1 (MQ=255)
                                                                                        ccTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAAccc                                                   >  2:178699/1‑141 (MQ=40)
                                                                                           ctGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCTAAc                                                >  2:251818/1‑141 (MQ=255)
                                                                                               aTCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATATACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTa                                            <  2:394022/141‑1 (MQ=18)
                                                                                                tCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGATTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAg                                           >  1:183236/1‑141 (MQ=255)
                                                                                                       cACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTg                                    >  1:181086/1‑141 (MQ=39)
                                                                                                                aaTAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAatgaaaac                           >  2:461892/1‑137 (MQ=255)
                                                                                                                          ttttCCTTTTATTTTGATGTACGTCTGATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGACAAAAAATTGGGGAATATATTTTAACCCAACGGTAAACCGTTGAATGATGAACCATAAcacc                 >  2:287151/1‑141 (MQ=11)
                                                                                                                           tttCCTTTTATTTTGTTGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcacca                <  2:361280/141‑1 (MQ=255)
                                                                                                                            ttCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTAcaccac               <  1:2304/141‑1 (MQ=39)
                                                                                                                             tCCTCTTACTTTGATGTACGTCCCATCAATACGCTATTTGTAACAAGCTTTATTCTGCTTTTTCTTGCAAATTTGACACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACg              <  1:324436/141‑1 (MQ=11)
                                                                                                                               cTTTTATTTTGATATACGTTTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGtt            <  1:52349/141‑1 (MQ=255)
                                                                                                                                ttttATTTTGATGGACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTCGTCCGTTGAATGATGAACGTTTACACCACGTTc           <  2:14616/141‑1 (MQ=255)
                                                                                                                                  ttATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTccc         <  1:214765/141‑1 (MQ=39)
                                                                                                                                      tttGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTaa     <  2:348159/141‑1 (MQ=40)
                                                                                                                                         gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAatct  >  2:12353/1‑139 (MQ=255)
                                                                                                                                         gATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAatat  >  2:55760/1‑141 (MQ=40)
                                                                                                                                            |                                                                                                                                         
TTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTGATGTACGTCTCATCAATACGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATAT  >  CP000730/36175‑36452

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑