Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 36,471 A→G 21.4% S27S (AGT→AGC)  USA300HOU_0026 ← IS431mec transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP00073036,4710AG21.4% 95.3 / 23.3 60S27S (AGT→AGC) USA300HOU_0026IS431mec transposase
Reads supporting (aligned to +/- strand):  ref base A (27/20);  new base G (7/6);  total (34/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

CGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGT  >  CP000730/36331‑36609
                                                                                                                                            |                                                                                                                                          
cGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATaa                                                                                                                                            >  2:263878/1‑141 (MQ=21)
 gCCATTTGTAATAAGCTTTTTTACTCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAAc                                                                                                                                           <  1:132722/141‑1 (MQ=255)
  ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACt                                                                                                                                          >  1:110358/1‑141 (MQ=21)
  ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACt                                                                                                                                          >  1:235741/1‑141 (MQ=21)
  ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACt                                                                                                                                          >  1:305753/1‑141 (MQ=21)
  ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGCTGATCGTCTACACCACGTTCCCTTAATATTTCAGATATATCACGATAAcc                                                                                                                                          >  1:160389/1‑140 (MQ=255)
  ccATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACt                                                                                                                                          >  2:269315/1‑141 (MQ=40)
  acATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGGTCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATGTCAGATATATCACGATAGCt                                                                                                                                          >  2:343402/2‑141 (MQ=11)
    aTTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACCTTCCCTTAATATTTCAGATATATCACGATAACTCa                                                                                                                                        >  1:122461/1‑141 (MQ=25)
    aTTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTGGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCa                                                                                                                                        <  2:298374/141‑1 (MQ=18)
     tttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCaa                                                                                                                                       >  1:264540/1‑141 (MQ=11)
     tttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCaa                                                                                                                                       <  2:329041/141‑1 (MQ=11)
     tttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCaa                                                                                                                                       >  1:363028/1‑141 (MQ=11)
     tttGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGCTAACTCaa                                                                                                                                       >  2:121894/1‑141 (MQ=21)
       tGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTGCAAAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATg                                                                                                                                     <  1:367602/141‑1 (MQ=11)
       tGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATg                                                                                                                                     <  2:122848/141‑1 (MQ=255)
       tGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCCGATATATCACGATAAATCAATg                                                                                                                                     >  2:10449/1‑141 (MQ=255)
       tGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATg                                                                                                                                     >  1:370347/1‑141 (MQ=40)
         taataaGCTTTTTTATGCTTTTTGCATCGAATTTTATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATgca                                                                                                                                   >  1:89319/1‑139 (MQ=11)
         taataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATgca                                                                                                                                   <  2:115258/141‑3 (MQ=11)
         taataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATATAAAATTGGGGCATATTCTTGAACCCAACGGTAGATCGTTGAATGATGAACGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATgca                                                                                                                                   >  1:211522/1‑139 (MQ=11)
         taataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGta                                                                                                                                   <  2:199253/141‑1 (MQ=40)
           ataaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGGTAACTCAATGtata                                                                                                                                 >  2:120543/1‑141 (MQ=255)
            taaGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTatat                                                                                                                                <  1:339836/141‑1 (MQ=40)
                 ttttttATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACCGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAg                                                                                                                           >  2:208074/1‑141 (MQ=37)
                       aTGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagta                                                                                                                     >  1:286432/1‑141 (MQ=35)
                        tGCTTTTTCTTCCAATTTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGAtagtag                                                                                                                    <  2:342631/141‑1 (MQ=25)
                          ggtgttgttcCAAAGTTGATACAAAAGTGGGGCATATTCCTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCGTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGcc                                                                                                                  <  2:160389/134‑1 (MQ=11)
                             tttCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAAc                                                                                                               <  2:309676/141‑1 (MQ=35)
                              ttcttcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCGTAGATAGTAGCCAACg                                                                                                              <  2:127356/141‑1 (MQ=25)
                                  tcCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTa                                                                                                          >  2:252134/1‑141 (MQ=35)
                                          tGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATa                                                                                                  >  1:359730/1‑141 (MQ=35)
                                            aTACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAAc                                                                                                >  2:295590/1‑141 (MQ=35)
                                             tACAGAATTGGGGCATATTCTTGACCCAAAAGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATAAAACGCTAACTCAATCTATATCTTACATAGTAGCCACCGGATACAGTATTAAct                                                                                               >  2:227361/1‑140 (MQ=11)
                                             tACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGCTTACACCCCGTTCCCTTAATATTTCAGATATATCACGCTAACTCAATGGATATCTTAGATAGTAGCCACCGGCTACAGTGATAACa                                                                                               >  2:369909/1‑141 (MQ=11)
                                               cAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATc                                                                                             <  1:333134/141‑1 (MQ=33)
                                                      ggggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTa                                                                                      <  2:20437/141‑1 (MQ=32)
                                                        ggCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTaaa                                                                                    >  1:288914/1‑141 (MQ=32)
                                                              ttCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATGACATCCTTGTTAAATTGttt                                                                              <  1:104879/141‑1 (MQ=17)
                                                                  tGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTatat                                                                          >  2:206222/1‑141 (MQ=32)
                                                                        cAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGaaa                                                                    >  2:332419/1‑141 (MQ=32)
                                                                           cGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAg                                                                 >  1:43728/1‑141 (MQ=32)
                                                                               aGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCa                                                             <  2:140675/141‑1 (MQ=32)
                                                                                        aaTGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACagaaga                                                    <  1:331334/141‑1 (MQ=32)
                                                                                          tgatgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACt                                                  >  2:41743/1‑141 (MQ=32)
                                                                                            atgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTGATACAGAAGACTct                                                >  2:126307/1‑140 (MQ=17)
                                                                                            atgaACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTcc                                                <  2:77929/141‑1 (MQ=32)
                                                                                               aaCGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCttt                                             <  2:324367/141‑1 (MQ=32)
                                                                                                 cGTTTACACCACGTTCTCTTAATATTTCAGATATATCACGATAGCTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCttttt                                           >  2:116264/1‑141 (MQ=12)
                                                                                                     tACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCATAGAGAGTAGCCAACGGCTACAGTGATAACATCCTTTTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTa                                       >  2:78985/1‑141 (MQ=12)
                                                                                                      acacCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGttca                                      >  1:98184/1‑139 (MQ=17)
                                                                                                        accacGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTaaaa                                    >  1:335005/1‑141 (MQ=32)
                                                                                                                cccTGAATAGTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACta                            <  1:191090/141‑1 (MQ=17)
                                                                                                                        atTTGAGATAGATCACGCTAACTCAATGTATCTCTTTGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAAGTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTGTTTGTTAAAATTATACTATAAATTCa                    <  1:126307/141‑1 (MQ=11)
                                                                                                                             agttatatCACGATAACTCAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACttt               <  1:106838/138‑1 (MQ=2)
                                                                                                                              gATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTg              >  1:375573/1‑141 (MQ=35)
                                                                                                                                  tatCACTATAGCTCACGGCATATCTTAGATAGTCGCCACCGGCTGTGGTGCTAACATCTCTGTTAAATTCTTTATATCTGAAATGGTGCATACAGATGACTCCTTTTTGCTAAAATTATATTATAAATTCAACTTTGCAAc          <  2:40976/141‑1 (MQ=255)
                                                                                                                                  tatCACGATAGCTCAAGGAATATCTTAGATAGTAGCCAACGACTACAGTGATGACTTCGTCGTTAAATTGTTTGTATCTCAAAAAATGCCAACAAAAGACTCCTATTTGTTACAATAGTATAATAAAATCAACTTTGcgaa          >  2:21977/1‑138 (MQ=2)
                                                                                                                                     caagATAACTTAATGCATATCTTAGATAGTAGCCAACAGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGa       <  2:127887/138‑1 (MQ=2)
                                                                                                                                         aTAGCTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCg   <  1:116264/141‑1 (MQ=25)
                                                                                                                                          tAACACAATGCATATCTTATATAGTAGCCAACGTCTACAGTTATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCTTACAGATGACTCCTTTTTGTTAAAATTATATTATAAATTCAACTTTGCAACAGAACCGt  <  2:13013/141‑1 (MQ=11)
                                                                                                                                            |                                                                                                                                          
CGCCATTTGTAATAAGCTTTTTTATGCTTTTTCTTCCAAATTTGATACAAAATTGGGGCATATTCTTGAACCCAACGGTAGACCGTTGAATGATGAACGTTTACACCACGTTCCCTTAATATTTCAGATATATCACGATAACTCAATGTATATCTTAGATAGTAGCCAACGGCTACAGTGATAACATCCTTGTTAAATTGTTTATATCTGAAATAGTTCATACAGAAGACTCCTTTTTGTTAAAATTATACTATAAATTCAACTTTGCAACAGAACCGT  >  CP000730/36331‑36609

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑