Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,590,608 G→T 10.0% L84L (CTG→CTT)  USA300HOU_2452 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,590,6080GT10.0% 126.2 / 2.0 51L84L (CTG→CTT) USA300HOU_2452hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (21/24);  new base T (4/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 4.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

ATCATTATCGTCTTTTTAACTTTTGGGTTAGTAGCTGTATTCACTCAACAAGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAATATTTTCGCAC  >  CP000730/2590474‑2590744
                                                                                                                                      |                                                                                                                                        
aTCATTATCGTCTTGTTAACTTTTGGGTTAGTAGCTGTATTCACTCAACAAGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCa                                                                                                                                     >  1:246129/1‑140 (MQ=255)
      aTCGTCTTTTTAACTTTTGGGTTAGTAGCTGTATTCACTCAACAAGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGa                                                                                                                               >  1:227337/1‑140 (MQ=255)
        tgTCTGTTTAACTTTTGTTGTGTTAGCTGTATTCACCCAACAATCTCCGTGGGGTTTCTCTTTTCCTATTTCAACTAACATTAGCTATTTACTCGCATTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATg                                                                                                                             <  2:223356/139‑1 (MQ=255)
        cGTCTTTTTAACTTTTGGGTTAGTAGCTGTATTCACTCAACAAGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATg                                                                                                                             <  2:487338/140‑1 (MQ=255)
               ttAACTTTTGGGTTAGTAGCTGTATTCACTCAACAAGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTAt                                                                                                                      >  1:146655/1‑140 (MQ=255)
               ttAACGTTTGGCCTAGTAGCTTTATTCACTCTACAAGCTCCGTGGGGTTTCTCTTTTCCGATTTCAATGAACACTAGCCATTTTCTCTCAGTTATTATTTCCCTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTAt                                                                                                                      <  2:440944/140‑1 (MQ=255)
                 aaCTTTTCGGTTAGTAGCTGTATTCACTCAACAATCTCCGTGGGGTTTCTTTTTTCCTATTTCAATGAACATTAGCTATTTATTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTc                                                                                                                    <  1:26410/140‑1 (MQ=255)
                      ttGGGTTAGTAGCTGTATTGACTAAACAAGCTCGGTGGGGTTTCTCTTTTCCTATTTCAATGAAAATTAGCTATTTACTCGCAGTTATTATTTCACTAGTTATTTTTCGTCTGTTGCACGAAGAAGTGTTTATTcacata                                                                                                               >  2:529093/1‑135 (MQ=255)
                                  cTGTATTCACTCAACAAGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTACTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCaa                                                                                                   >  2:281375/1‑140 (MQ=255)
                                       ttCACTCAACAAGCTCTGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGt                                                                                              >  1:273931/1‑140 (MQ=255)
                                         ctcTCAACAAGCTCCGTGGGGTTTCTCTTTGCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTg                                                                                            <  2:219268/138‑1 (MQ=255)
                                                 aaGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCt                                                                                    <  1:48416/140‑1 (MQ=255)
                                                    caccggtgggTTTCTCTTTTTCTATTTCAATGAATATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTaaa                                                                                 <  2:207837/133‑1 (MQ=255)
                                                    cTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTaaa                                                                                 <  2:462119/140‑1 (MQ=255)
                                                      ccGTGTGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTgaaataat                                                                               <  2:54247/140‑8 (MQ=255)
                                                       cGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAatat                                                                              <  1:433280/140‑1 (MQ=255)
                                                         tGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTCTTATTTCACTAGCTCTTTTTAGTATGATGCATGAAGATGCGTTTAGTCCCATGCTACGTTCGCAAATCGTTGCTAGTGCTACATATaa                                                                            >  2:200489/1‑140 (MQ=255)
                                                           gggTTTCTCTTTTCCTATTTCAATGACCATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAAt                                                                          <  2:7168/140‑1 (MQ=255)
                                                            ggTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATg                                                                         <  2:146655/140‑1 (MQ=255)
                                                            ggTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATg                                                                         >  1:62914/1‑140 (MQ=255)
                                                             ctttCTCTTTTCCTATTTCAATTAACATTAGTTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATgg                                                                        <  1:498980/139‑1 (MQ=255)
                                                              tttCTCTTTTCCTATTTTAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGc                                                                       <  1:476515/140‑1 (MQ=255)
                                                                         cTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTtata                                                            <  1:380946/140‑1 (MQ=255)
                                                                         cTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTtata                                                            >  2:320654/1‑140 (MQ=255)
                                                                          aaTTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATACAAATGATACGTTCGTAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTatat                                                           <  2:60456/139‑1 (MQ=255)
                                                                             ttCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCAt                                                        <  2:246129/140‑1 (MQ=255)
                                                                             ttCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCAt                                                        >  2:133069/1‑140 (MQ=255)
                                                                                  tGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGAGTTTATTCAAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGACATATTCTTATATCATTTaca                                                   >  1:47137/1‑140 (MQ=255)
                                                                                   gAACACTAGATCTTGACCTGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGAGACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTacac                                                  <  2:216072/140‑1 (MQ=255)
                                                                                     aCATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTTTTTTTTTTTATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATATATGGCATATTCTTATATCATTTACACTa                                                >  2:347844/1‑140 (MQ=255)
                                                                                     aCATTAGCTATTTACTCGCAGTTATTATTTCACTACCTACTTTTCGTATGATGCATGAAGATGCGCTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTa                                                >  2:115927/1‑140 (MQ=255)
                                                                                        ttAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATTATACGTTCGCAAATAGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATAATTTACACTAAgg                                             >  1:49576/1‑139 (MQ=255)
                                                                                         tAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTGGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTACgtg                                            >  2:54850/1‑140 (MQ=255)
                                                                                         tAGCTAGTGACGCGCAGTTATTATTTCGCTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAgtg                                            >  2:404915/1‑140 (MQ=255)
                                                                                            cTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTTTTTTTTTTTTTGATGATGAGTTTCTTCAAATGATACGTTTGTGTATTGTTGCTAGTACTAATTATATATTGCATATTGTTATATCAttttctatagttgttg                                         >  2:165059/1‑127 (MQ=255)
                                                                                             ttgttacgtgtaGTTATTATTTCCCGAGCTATCTTTCGTTATATGCATTAATATGCTTTATTTCCAATGAGTCGGTCGCAAATCGTTGCTATTGCTAAATATAAATGGCATATTCATATATCATTTACACTTAGTGTCGt                                        <  2:59491/129‑1 (MQ=255)
                                                                                                      gCAGTTATTATTTCACTAGCTATTTTTTTTTTTTTTTTTGATGATAGGTTTATTCCAATGATACTTTCGCAAATCGTTGTTAGTGCGAGTTATCCTTGGCTTATTATTATTTCGTTTACATTAAGTGCTGTACTTttctt                               >  2:386184/1‑140 (MQ=255)
                                                                                                      gCAGTTATTATTTCACTAGCTATTTTTTTTTTTTTTTATGAAGATGAGTTTATTCCAATGATACGTTCGCAAATCGTTGCTTGTGCTAAATATAAATGTCATATTTTTATATCATTTACATTAAGTTTATTACTCttttt                               >  2:488688/1‑140 (MQ=255)
                                                                                                           ttttattTCTCTACCTATTTTTCGTCTTATGCATGAAGATTCTTTTATTCCAAGTATACGTTCTCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACttt                          <  1:218590/138‑1 (MQ=255)
                                                                                                             ttattTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTa                        >  2:52416/1‑140 (MQ=255)
                                                                                                             ttattTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTa                        >  1:290037/1‑140 (MQ=255)
                                                                                                                  tCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCa                   <  1:470403/140‑1 (MQ=255)
                                                                                                                          tATTTTTCGTCTGATGCATGAAGATGCGTTTATTCTAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGTATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAata           <  1:318995/140‑1 (MQ=255)
                                                                                                                          tATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAata           <  1:362895/140‑1 (MQ=255)
                                                                                                                               ttCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCATTATTTTc      >  1:149254/1‑140 (MQ=255)
                                                                                                                               ttCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAATATTTTc      <  2:414604/140‑1 (MQ=255)
                                                                                                                               ttCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCGTTTTACTTATAAATCATTTCAATATTTTc      <  1:334914/140‑1 (MQ=255)
                                                                                                                                 cGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGTTAAATATAAATGGCATATTCTTATATTATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAATATTTTCGc    <  1:441004/140‑1 (MQ=255)
                                                                                                                                 cGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAATATTTTCGc    >  1:191874/1‑140 (MQ=255)
                                                                                                                                 cGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTAATAAAATTAAAACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAATATTTTCGc    >  1:192006/1‑140 (MQ=255)
                                                                                                                                   tCTGATGCATGAAGATGCGATTATTCCAATATTACGTTCGCAAATCGTTGCTAGAGCTAAAAATAAATCGCCTGTTCTTATCTCATTTACAGTAGGTGTCGTACTCTTTTTACTTTTAAATACTTTCATTATTTTGGCAc  >  2:27255/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                        
ATCATTATCGTCTTTTTAACTTTTGGGTTAGTAGCTGTATTCACTCAACAAGCTCCGTGGGGTTTCTCTTTTCCTATTTCAATGAACATTAGCTATTTACTCGCAGTTATTATTTCACTAGCTATTTTTCGTCTGATGCATGAAGATGCGTTTATTCCAATGATACGTTCGCAAATCGTTGCTAGTGCTAAATATAAATGGCATATTCTTATATCATTTACACTAAGTGTCGTACTCTTTTTACTTTTAAATCATTTCAATATTTTCGCAC  >  CP000730/2590474‑2590744

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: ‑