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% 154.6 / ‑6.5 49S204L (TCA→TTA) USA300HOU_1186CodY family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (22/26);  minor base A (1/0);  total (23/26)
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.

TGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTC  >  CP000730/1274077‑1274344
                                                                                                                                   |                                                                                                                                        
tGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGc                                                                                                                                 <  2:426968/141‑1 (MQ=255)
        aaaaaGAAGCGCGCGATAAAGCTGCTATTAGAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTGGAAGAACTTGGCGGTACGGGAGGCCTATTAATCGCATTAAAAGTTGCAGATagag                                                                                                                         <  2:333752/141‑1 (MQ=255)
         aaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGt                                                                                                                        <  1:658274/141‑1 (MQ=255)
         aaaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGt                                                                                                                        <  1:736475/141‑1 (MQ=255)
          aaaGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGtt                                                                                                                       <  2:467464/141‑1 (MQ=255)
           aagaagCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTg                                                                                                                      <  1:362431/141‑1 (MQ=255)
                 cgcgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTa                                                                                                                >  2:313184/1‑141 (MQ=255)
                   cgcgATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACt                                                                                                              >  1:131382/1‑141 (MQ=255)
                       aTAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGAt                                                                                                          <  1:757036/141‑1 (MQ=255)
                       aTAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTATGAAAAAGAAGCGATTGAACATATCTTTGACGAACTTGGCGGTACGGAAGGCCTGTTAATGGCGTTAAAAGTTGCAGATAGAGTTGGTATTACTAggt                                                                                                          >  1:214903/1‑139 (MQ=255)
                        tAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATc                                                                                                         <  2:94443/141‑1 (MQ=255)
                        aaaaGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATc                                                                                                         <  2:392687/140‑1 (MQ=255)
                          aaGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATAACAAGTTGCAGATAGAGTTGGTATTACTAGATCTg                                                                                                       >  1:722050/1‑141 (MQ=255)
                           aGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGTTAGAGTTGGTATTACTAGATCTGt                                                                                                      >  1:227958/1‑141 (MQ=255)
                                ctATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTg                                                                                                 <  2:541488/141‑1 (MQ=255)
                                    tACAATGGCAAATAATTCATTAGCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaaa                                                                                             <  1:69990/141‑1 (MQ=255)
                                    tACAACGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAAGCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTaaa                                                                                             <  2:204224/141‑1 (MQ=255)
                                      cAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATg                                                                                           >  1:331393/1‑141 (MQ=255)
                                       aaTGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGc                                                                                          >  1:324473/1‑141 (MQ=255)
                                        aTGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCa                                                                                         >  2:418887/1‑141 (MQ=255)
                                         tGGCAATTAATTCATTATCTTGTTCTGAAAAAGAAGCGATTGAACATTTCTTTCAAGAACTTGGCAGTACGGAAGGCCTATTAATCGCATTAAAGTTTGCAGTTAGAGTTGGTAATACTAGATCTGTAAGTGTAAATTCAc                                                                                        <  2:135607/141‑1 (MQ=255)
                                           gCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGACCCCGGAAGGTTTGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTa                                                                                      <  1:360717/141‑1 (MQ=255)
                                            cAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTAc                                                                                     <  2:65439/141‑1 (MQ=255)
                                              attaattCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGt                                                                                   >  2:511443/1‑141 (MQ=255)
                                                taattCATTATCTTATTCGGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATGAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTaa                                                                                 <  2:364242/141‑1 (MQ=255)
                                                      aTTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGa                                                                           >  1:236834/1‑141 (MQ=255)
                                                               ttCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTgg                                                                  >  1:425791/1‑141 (MQ=255)
                                                                    aaaaaGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCCCTACGTAAATTAGAAAGTGCTGGTGTaa                                                             >  1:521300/1‑141 (MQ=255)
                                                                           agCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATc                                                      >  1:236698/1‑141 (MQ=255)
                                                                           agCGAGTGAACAGATCTTTGAAGCACTTGGCGGTACGGAAGGCCTATTAAGCGCACTAAAAGTTGCAGATAGAGGTGGTATTACTAGATCTGTAATTATAACTGCACTACGTAAATGAGAAAGTGCTGCTGTGCTTGCATc                                                      >  2:475169/1‑141 (MQ=255)
                                                                               aTTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGt                                                  <  1:313184/141‑1 (MQ=255)
                                                                                 tGAACATATCTATGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATAACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTc                                                <  1:303501/141‑1 (MQ=255)
                                                                                    aCATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAACTTGCAGATAGGGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCttt                                             <  2:47465/141‑1 (MQ=255)
                                                                                       tatCTTTGAAGAACATGGCAGTACGGAAGGCCTATTCATCGCATTAAAAGTTGCAGATACAGTTGGTATTACTAGATCTGTAGTTGTAAATGCACTACGTGAATTAGTAAGTGCTGGTGTACTTGAATTACGTTCTTTAgg                                          >  2:424625/1‑141 (MQ=255)
                                                                                        atCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGa                                         <  2:331393/141‑1 (MQ=255)
                                                                                          cTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAAt                                       <  1:590924/141‑1 (MQ=255)
                                                                                            ttGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGGTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTTGGAATGa                                     >  2:671823/1‑141 (MQ=255)
                                                                                                 gaaCTTGGCGGTAGGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATGGAGGTGGTATTACTAGATGTGTAATTGTAAATGCACTACGTAGATTAGAAAGTGCTGGTGTAATTGAATCAGGTTCTTGAGGAGTGAGAGGt                                >  1:189498/1‑141 (MQ=255)
                                                                                                 gaaCTTGGCGGTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGGGCTGGTGTAATTGAATCACGTTTTTTAGGAATGAAAGGt                                >  2:668961/1‑141 (MQ=255)
                                                                                                   aCTTGGCGGCACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTAc                              >  2:408053/1‑141 (MQ=255)
                                                                                                    cTTGGCGGTACGGAAGTCATATTAAGCGCATTAAAAGTGTCAGATCGGGTTGTGATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAgtacct                             <  1:746012/141‑6 (MQ=255)
                                                                                                          ggTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGGTAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAATGGTACtttaaaa                       <  2:394314/141‑5 (MQ=255)
                                                                                                          ggTACGGAAGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCAtt                       <  2:432144/141‑1 (MQ=255)
                                                                                                                  aGGCCTATTAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTaa               >  1:291635/1‑141 (MQ=255)
                                                                                                                      cTATTAATCGCATTAAAAGTCGCAGATAGAGTTGTTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGTTGTAATTGAATCACGTTCTTTAGTAATGAAAGGTACTTTCATTAAAGTTaaaaaa           <  2:577624/141‑1 (MQ=255)
                                                                                                                          tAATCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACCACGTAAATTAGCAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaaa       <  2:381240/141‑1 (MQ=255)
                                                                                                                             tCGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAAt    >  1:358549/1‑141 (MQ=255)
                                                                                                                              cGCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGaaaaaat   >  2:710253/1‑139 (MQ=255)
                                                                                                                               gCATTAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAAttt  >  1:478269/1‑140 (MQ=255)
                                                                                                                                   |                                                                                                                                        
TGAAGTAGAAAAAGAAGCGCGCGATAAAGCTGCTATTACAATGGCAATTAATTCATTATCTTATTCTGAAAAAGAAGCGATTGAACATATCTTTGAAGAACTTGGCGGTACGGAAGGCCTATTAATCGCATCAAAAGTTGCAGATAGAGTTGGTATTACTAGATCTGTAATTGTAAATGCACTACGTAAATTAGAAAGTGCTGGTGTAATTGAATCACGTTCTTTAGGAATGAAAGGTACTTTCATTAAAGTTAAAAAAGAAAAATTC  >  CP000730/1274077‑1274344

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑