Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,274,208 C→T 100% S204L (TCA→TTA)  USA300HOU_1186 → CodY family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,274,2080CT100.0% 127.3 / ‑6.5 44S204L (TCA→TTA) USA300HOU_1186CodY family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (1/1);  major base T (14/26);  minor base G (0/2);  total (15/29)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAA  >  CP000730/1274078‑1274339
                                                                                                                                  |                                                                                                                                   
gAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAAGCGCATTAAAAGTTGCa                                                                                                                           <  1:480949/141‑1 (MQ=255)
aaaGTAGAGAAAGGAGCGCGCGATAAAGCTGCTAGTACAATGACAATTAATGTATTATTATATCCTGAAAACGAACCGATTTAACATATCTTTGGAAAACTTGGCGTGACGGAAGGCCTATTAATCGCATTAAAAGTTGCa                                                                                                                           <  2:419802/140‑1 (MQ=255)
  aGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGa                                                                                                                         <  2:326837/141‑1 (MQ=255)
  aGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGa                                                                                                                         <  1:709542/141‑1 (MQ=255)
     aGAAAAAGAAGCGCGCGATAAGGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGACGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATag                                                                                                                      <  2:466763/141‑1 (MQ=255)
       aaaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGGTagag                                                                                                                    >  2:533233/1‑141 (MQ=255)
        aaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGt                                                                                                                   >  1:761085/1‑141 (MQ=255)
          aagaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTATGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGAAGCTAGGGTTg                                                                                                                 >  2:512776/1‑141 (MQ=255)
             aagCGCGTGATAAAGCTGCTATTACAATGGCAATTAATTCATTATTTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGTCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTa                                                                                                              <  2:404724/141‑1 (MQ=255)
               gcgcgcGATAAAGCTGCTATTACAATGGCAATTAATTCATCATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACAGAAGGCCGATTAATCGCATTAAAAGTTGCCGATAGAGTTgggctt                                                                                                            >  2:818486/1‑137 (MQ=255)
                cgcgtgATAAAGCTGCTATTACGAGGGCAATTAATGTAGTAGTGGATCTTAGAACAATTGCGATTGTACGTACCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATGAAAAGTTGCATATAGATTTGGTATTa                                                                                                           <  2:93201/141‑1 (MQ=255)
                cgcgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCAGTACGTAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTa                                                                                                           >  2:830028/1‑141 (MQ=255)
                    cgATTAAGCTGCTATTACAATGCCAATTATTTCATTATCATATTGTGTCGAGGTAGCTTGGGAACATAGCGGTGAAGAGCTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGGTGCGGATAGAGTTGGTATTACGAg                                                                                                       <  2:48741/141‑1 (MQ=255)
                        aaaGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCGGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCt                                                                                                   <  1:447040/141‑1 (MQ=255)
                         aaGCTGCTATTACAAGGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAACACTTTCTGATGGAGGGGGTATTACTAGATCTg                                                                                                  <  1:206955/141‑1 (MQ=255)
                            ctgctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTaa                                                                                               <  1:836994/141‑1 (MQ=255)
                              tctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGTTCTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAtt                                                                                             <  2:742231/140‑1 (MQ=255)
                              gctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAAtt                                                                                             <  1:742821/141‑1 (MQ=255)
                                  ttACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGCACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaa                                                                                         <  1:584839/141‑1 (MQ=255)
                                     aaaTGGCAATTAATTCATTATCTTATGCTGAAAAAGAAGCGATTGAACATATCGTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATg                                                                                      <  2:753094/140‑1 (MQ=255)
                                        tGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCAc                                                                                   <  1:469580/141‑1 (MQ=255)
                                           cAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTAc                                                                                >  1:770821/1‑141 (MQ=255)
                                             attaattCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGt                                                                              <  2:321470/141‑1 (MQ=255)
                                                  ttCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAAtt                                                                         <  2:323167/141‑1 (MQ=255)
                                                    taatATCTCATTCTAAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGACTATTAATCGTATTAAAAGTTTAAGATAGAGTTAGTATTAGTAGATCTGTAATTTTAAATGCACTACGTAAATTAg                                                                       <  2:454166/138‑1 (MQ=255)
                                                    cATTATCTTGTTCAGAAAAAGAAGCGATTGAACATATCGTTGAAGAACTTGGTGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGTTATTACTAGATCTGTAATTGTAGATGCACTACGTAGATTAg                                                                       <  2:495868/141‑1 (MQ=255)
                                                    cATGATCTTATTCTGAAAAAGAAGCGATTGAACGTATCTTTGAAGAACGTGGGGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAg                                                                       <  2:42859/141‑1 (MQ=255)
                                                     aTTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGa                                                                      >  1:150822/1‑141 (MQ=255)
                                                               tCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTTCTGgt                                                            <  2:529421/141‑1 (MQ=255)
                                                                        gaagCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGAAAGAGTTGGTATTACTCGATCTGTAATTGGACATGCACTACGTAAATTAGAAAGTGCTGGTGAAATTGaa                                                   >  2:29845/1‑141 (MQ=255)
                                                                             gATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACg                                              >  2:318538/1‑141 (MQ=255)
                                                                                 gAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAGTTGAATCACGTTCt                                          >  1:774834/1‑141 (MQ=255)
                                                                                          tttGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATg                                 >  1:509457/1‑141 (MQ=255)
                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGGATGGAAGGTACt                        >  2:454555/1‑141 (MQ=255)
                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                        <  2:747325/141‑1 (MQ=255)
                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                        <  2:69302/141‑1 (MQ=255)
                                                                                                   cTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACt                        <  2:226723/141‑1 (MQ=255)
                                                                                                           tACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaa                <  1:353072/141‑1 (MQ=255)
                                                                                                            tgggAAGGCCTATTAAACGCTTTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTaaa               <  2:401904/139‑1 (MQ=255)
                                                                                                             cGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTATTTAGGAATGAAAGGGACTTTCATTAAAg              >  1:369840/1‑141 (MQ=255)
                                                                                                              ggAAGGCCTATTAATAGCATTAAAGGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGGAAGGTACTTTCATTAAAGt             <  2:409519/141‑1 (MQ=255)
                                                                                                                 aGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAGTTGGGTCTCGTGCTTTAGGAATGAAAGGTACTTTCCTTAAGGTGaa          >  1:668769/1‑141 (MQ=255)
                                                                                                                  ggCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTaaa         >  1:20243/1‑141 (MQ=255)
                                                                                                                         tAATCGCACGAAAAGTGCGAGATGTAGTTGTTATTACTAGATCTTGAATTGTAAATGCACTACGTAAATTAGAAAGTGCTTGTGTAATTGAATCACGTTTTTTAGGAATTAAAGGTACTTTCATTAAAGTTAAAAAAGaaa  <  2:735745/141‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                   
GAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAA  >  CP000730/1274078‑1274339

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: ‑