Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,794,352 A→T 9.6% Y431N (TAT→AAT)  USA300HOU_1678 ← hypothetical membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,794,3520AT 9.6% 110.6 / 2.4 38Y431N (TAT→AAT) USA300HOU_1678hypothetical membrane protein
Reads supporting (aligned to +/- strand):  ref base A (15/19);  new base T (2/2);  total (17/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCTTGGTAATTTTTATTGATTGGTGACGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTAATAAAATAATTAAAATGATTACATGTATCGTATAAA  >  CP000730/1794215‑1794489
                                                                                                                                         |                                                                                                                                         
ctctTGGTAATTTTTATTGATTGGTGACGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATTATg                                                                                                                                        <  2:402511/141‑1 (MQ=255)
ctctTGGTAATTTTTATTGATTGGTGACGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATg                                                                                                                                        >  1:413701/1‑141 (MQ=255)
 tctTGGTAATTTTTATTGATTGGTGACGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATTATGa                                                                                                                                       <  1:59717/141‑1 (MQ=255)
    tGGTAATTTTTATTGATTGGTGACGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACa                                                                                                                                    <  1:261877/141‑1 (MQ=255)
               attgactgGTGACGGATGATGCATATAATGGTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATGGGTTGTTTTAATAACTGATCTCTTTTTTCATGTTCATAATGAACATAAATAAATGc                                                                                                                         <  2:99887/141‑1 (MQ=255)
                ttgattgGTGACGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCa                                                                                                                        <  2:286521/141‑1 (MQ=255)
                          aCGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGatata                                                                                                              <  1:346698/141‑1 (MQ=255)
                           cGGATGATGCAGATAATGTTTAAACGGCAATGATTCCACTGTATAAACCACTTGTCGTGGATGATCTTTAATGTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATACTGAACATAAATAAATGCACTAAGatatat                                                                                                             >  2:13421/1‑141 (MQ=255)
                              atgatgCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATcac                                                                                                          <  2:224548/141‑1 (MQ=255)
                                 atgCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGc                                                                                                       <  1:434232/141‑1 (MQ=255)
                                  tgCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCt                                                                                                      <  1:71366/141‑1 (MQ=255)
                                   gCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTa                                                                                                     <  2:388506/141‑1 (MQ=255)
                                            gTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTg                                                                                            <  2:48550/141‑1 (MQ=255)
                                              tCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGAt                                                                                          <  1:479346/141‑1 (MQ=255)
                                                 aaCGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTAATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTCAAACTAGTGATGCa                                                                                       >  2:281088/1‑141 (MQ=255)
                                                  aCGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCAc                                                                                      <  1:219158/141‑1 (MQ=255)
                                                    ggCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATACACTAAGATATATCACAGCTAAAACTAGTGATGCACCt                                                                                    >  2:490693/1‑141 (MQ=255)
                                                      cAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCttt                                                                                  >  1:130123/1‑141 (MQ=255)
                                                               cACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAAtt                                                                         <  2:234312/141‑1 (MQ=255)
                                                                aCTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATACACCTTTAATAAAATTa                                                                        >  2:316259/1‑141 (MQ=255)
                                                                           ctctTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACAttgattga                                                             >  2:145252/1‑141 (MQ=255)
                                                                            tctTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGAc                                                            <  1:468301/141‑1 (MQ=255)
                                                                             ctTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACt                                                           >  1:147254/1‑141 (MQ=255)
                                                                                gTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTtat                                                        >  1:24130/1‑141 (MQ=255)
                                                                                    tGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATAttt                                                    <  1:208948/141‑1 (MQ=255)
                                                                                              ttAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATTTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATTCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATGCt                                          >  2:26404/1‑141 (MQ=255)
                                                                                                 aTTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCtttt                                       >  1:133234/1‑141 (MQ=255)
                                                                                                    tgttgtTTTAATAACTGAACTCTTTTTTTTTTTTTTTTTTGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATCAACATTTATTTACTTATTTTTCCGAAATTCTTTtatt                                    >  2:65033/1‑139 (MQ=255)
                                                                                                      ttgttTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTtaataa                                  >  1:202853/1‑141 (MQ=255)
                                                                                                         ttttAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTaataaaat                               <  2:42202/141‑1 (MQ=255)
                                                                                                             aataaCTGAACTCTTTTTTTTTTTTTTTTTTGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATAGATTGACTTATATTTCCGAAATTCTTTTATTAAAAGAAtt                           >  2:444574/1‑141 (MQ=255)
                                                                                                                 aCTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTAATAAAATAATTaaaa                       <  1:203915/141‑1 (MQ=255)
                                                                                                                  cTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGACTCTTTAATAAAGTTCCAATTGCTTGCGTTATCTTTAAGAAGTTTTTTTCATAAAATAATTAACAt                      >  1:425344/1‑141 (MQ=255)
                                                                                                                      aCTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTAATAAAATAATTAAAATGAtt                  <  1:301166/141‑1 (MQ=255)
                                                                                                                          ttttttCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTAATAAAATAATTAAAATGATTACAt              <  2:439448/141‑1 (MQ=255)
                                                                                                                           tttttCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGCCTTATATTTCCGAAATTCTTTTAATAACATAATTAAAATGATTACATg             <  2:130123/141‑1 (MQ=255)
                                                                                                                                   gTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTAATAAAATAATTAAAATGATTACATGTATCGtat     >  1:51955/1‑141 (MQ=255)
                                                                                                                                      cATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTAATAAAATAATTAAAATGATTACATGTATCGTATaaa  >  1:166826/1‑141 (MQ=255)
                                                                                                                                         |                                                                                                                                         
CTCTTGGTAATTTTTATTGATTGGTGACGGATGATGCATATAATGTTCAAACGGCAATGATTCCACTGTATAAACCTCTTGTCGTGGATGATCTTTAATTTGTTGTTTTAATAACTGAACTCTTTTTTCATGTTCATAATGAACATAAATAAATGCACTAAGATATATCACAGCTAAAACTAGTGATGCACCTTTAATAAAATTAACATTGATTGACTTATATTTCCGAAATTCTTTTAATAAAATAATTAAAATGATTACATGTATCGTATAAA  >  CP000730/1794215‑1794489

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: ‑