Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 479,553 G→A 100% A194T (GCA→ACA)  USA300HOU_0458 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730479,5530GA98.4% 184.5 / ‑5.6 61A194T (GCA→ACA) USA300HOU_0458hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (26/33);  total (27/34)
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
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.

GTGATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479416‑479686
                                                                                                                                         |                                                                                                                                     
gTGATGCAATAAAAGATGAACGAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTATATCGAGTGGGACAATGCCGAAGCGTGAGCAAAGTTTTTACcatacat                                                                                                                                    >  1:291101/1‑141 (MQ=255)
  gaggccataataGATGAACCAGGTGGCCCACTGATCCAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGTTCAATTTTTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATgg                                                                                                                                  <  2:277277/135‑1 (MQ=255)
   aTGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGt                                                                                                                                 <  2:484778/141‑1 (MQ=255)
         aaataAATGAACAGTGTGAGCCCCTTAGCGAACAAGTGAACCGTCAAATGAGTAAATGGACGAAACTTTATATCGATCAATTTCGATCGAGTTAGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCAtt                                                                                                                           <  2:482940/140‑1 (MQ=255)
              gATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAGTGATTAAATGGACGAAACTTGATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcg                                                                                                                      <  1:85435/141‑1 (MQ=255)
              aaTGAACAAGGCGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATCAAATGGACGAAACTTTATATCGATCAATTTCTAGCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAgcg                                                                                                                      <  1:215770/140‑1 (MQ=255)
               aTGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGGGCAAAGTTTTTACCATACATGGTTGCATTTAgcgc                                                                                                                     <  1:444183/141‑1 (MQ=255)
                tGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCa                                                                                                                    >  2:421072/1‑141 (MQ=255)
                tGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCa                                                                                                                    <  1:421072/141‑1 (MQ=255)
                    cAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACAt                                                                                                                <  2:103715/141‑1 (MQ=255)
                    cAAGGTGAGCCACTTAGCGAACAAGTGAATAGTAAAATGATTAAATGGACGAAACGTTATATCGATCAATTTGTAACGAGTTGGACAATGCGGAAGCGTGAGCACAGATTTGACACAGCATGGCTGCaatacacgcacaag                                                                                                                >  2:146392/1‑128 (MQ=255)
                       ggggAGCCACTTAGCGAACCAATGGATCGTCAAATGATTAAATGGACGAAACTTTATATAGATCAAGTTCTATCGAGTTGGACAGTGCAGACGCGTGAGCAAGGTTTTTACCATACATGGTTGCATTGAGCGCAACATGAc                                                                                                             >  2:145842/4‑141 (MQ=255)
                       ggTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTCCCATACATGGTTGCATTTAGCGCAACATGAc                                                                                                             >  1:83275/1‑141 (MQ=255)
                        gTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGAcc                                                                                                            >  2:409061/1‑141 (MQ=255)
                         tGAGCCACTCAGCGAACAAGTGAATCGTCAAACGCATTAATGGAAGAATCTTCATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACCTGGTTGCATTTAGCGCAACATGACCa                                                                                                           <  2:394086/141‑1 (MQ=255)
                          gAGCCATTTAGCGAACAAGTTAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCAt                                                                                                          <  1:351744/141‑1 (MQ=255)
                          gAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCAt                                                                                                          <  1:97624/141‑1 (MQ=255)
                          gAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCAt                                                                                                          >  1:514320/1‑141 (MQ=255)
                               aCTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCACTTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCCTACATGCCTGCATTTAGCGCAACATGACCAAAGctt                                                                                                     >  2:205800/1‑141 (MQ=255)
                               aCTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTGTTTACCATACATGGTTGCATTTAGCGCAACATGACCAAAGttt                                                                                                     >  2:205882/1‑141 (MQ=255)
                                cTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGtttt                                                                                                    >  2:16773/1‑141 (MQ=255)
                                       aaCACGTGAATCGTCAAATGATTAAATGGACGAAACTTTATAACGATCAATTTCTATCGGGTTGGCCAATGCCGAAGCGGGAGCGAAGGTTTTACCATACATGGTTGCGTTTAGCGCAACATGACCCGAGACTTACTAAAg                                                                                             >  2:69894/1‑141 (MQ=255)
                                       aaCAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGATCATAGTTTTACTAAAg                                                                                             >  1:200441/1‑141 (MQ=255)
                                       aaCAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACAGGACCATAGTTTTACTAAAg                                                                                             <  1:335579/141‑1 (MQ=255)
                                        aCAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGc                                                                                            >  1:160118/1‑141 (MQ=255)
                                        aCAAGTGAAGCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGc                                                                                            <  2:102781/141‑1 (MQ=255)
                                              gcaTCGTCAAATGATTAAATGGACGAAACTTTACATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAgcg                                                                                      <  2:115426/139‑1 (MQ=255)
                                              gagacGTTAAATGATTAGATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCACAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAgcg                                                                                      <  2:251683/137‑1 (MQ=255)
                                               aaTCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGATGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATAACCATAGTTTTACTCAAGCACAgcgc                                                                                     >  2:343347/1‑141 (MQ=255)
                                                   gTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAGGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTACCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAg                                                                                 >  1:14262/1‑141 (MQ=255)
                                                     cAAATGATTAAATGGACGAAACTTTATATCGAGCAATTTCTATCGAGTTGGAAAATGCCGAAGCGTGAGGAAAGTTTTTACCATACATGGTTGCATTTAGCGTAACATGAACATAGTTTTACTAAAGAACAGCGCAAAGTg                                                                               >  2:362657/1‑141 (MQ=255)
                                                        aTGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGCGAtt                                                                            >  1:138871/1‑141 (MQ=255)
                                                             tAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  1:163996/141‑1 (MQ=255)
                                                             tAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  2:52376/141‑1 (MQ=255)
                                                             tAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  2:448479/141‑1 (MQ=255)
                                                             tAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATCCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAGGTGATTAAAgg                                                                       >  1:108022/1‑141 (MQ=255)
                                                             tAAAGGGACGAAACTTGATATCGATCAATTGCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCAGAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAgg                                                                       <  1:231579/141‑1 (MQ=255)
                                                                            ttATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATcc                                                        >  2:75252/1‑141 (MQ=255)
                                                                             tataTCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCt                                                       <  2:219453/141‑1 (MQ=255)
                                                                               tatCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGa                                                     <  2:216681/141‑1 (MQ=255)
                                                                                    aTCAATTTCTATCGAGTTGGACAATGCCGAAGCTTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCCTAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTGCCCAATGATCCTGAAATGa                                                <  2:313810/141‑1 (MQ=255)
                                                                                     tCAGTTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGAc                                               <  2:63727/141‑1 (MQ=255)
                                                                                        atgtCTATCGAGTTGGACAATGCCGAAGCGTGAACAAAGTTTTTACAATACATGGTTGCATTTAGCGCAACACAACCATCGATTTACTAAAGCAAAAGGCCACGTGACTAAAGGCTTACCCAAGGTACCAGAAATgcgtaa                                            >  2:334791/4‑136 (MQ=255)
                                                                                         tttCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCCTGGGTGATTGCGTGTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATa                                           <  1:243240/141‑1 (MQ=255)
                                                                                         tttCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATa                                           >  1:25292/1‑141 (MQ=255)
                                                                                         tttCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATa                                           <  2:555722/141‑1 (MQ=255)
                                                                                         tttCGATCGAGTTGGACAATGCCGAAGCGTGCGCAACGTTTATACCATACATGGTTGAATCAAGCGCAACTTGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATGAAAGGCTGACCCATTGATCCTGAAATGACGATa                                           <  2:555452/141‑1 (MQ=255)
                                                                                           tCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCTTACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATaga                                         <  2:287613/141‑1 (MQ=255)
                                                                                                cGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAg                                    <  1:435206/141‑1 (MQ=255)
                                                                                                 gAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAAAGTCAGt                                   >  1:376971/1‑141 (MQ=255)
                                                                                                  aGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGGGTCAGtt                                  >  2:17282/1‑140 (MQ=255)
                                                                                                  aGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTa                                  >  1:470110/1‑141 (MQ=255)
                                                                                                  aGTTGGACAATGCCGAAGCGGGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTa                                  <  2:125139/141‑1 (MQ=255)
                                                                                                       gACAATCGCGAAGCGTGAGCAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAAc                             <  2:72040/141‑1 (MQ=255)
                                                                                                              ccGAAGCGTGAGCAAAGTTTTTACCATACCTGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCAtttt                      <  2:410271/141‑1 (MQ=255)
                                                                                                                        agtaaaGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATc            <  1:371353/138‑1 (MQ=255)
                                                                                                                          cAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGGACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCA‑TTTTCAATAGATCAgg         >  1:338330/1‑141 (MQ=255)
                                                                                                                          cAAAGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGGATTAACTCATTTTTCAATAGATCAg          >  1:202744/1‑141 (MQ=255)
                                                                                                                            aaGTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCCTTTTTCAATAGATCCGGa        >  1:245734/1‑141 (MQ=255)
                                                                                                                              ttttttCCCATACATGGTTGCATTTAGCGCAACATGACCATAGCTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAg      <  2:520822/140‑1 (MQ=255)
                                                                                                                              gTTTTTACCATACATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGCTCAGGAAg      >  1:354234/1‑141 (MQ=255)
                                                                                                                                  ttACCATAAATGGTTGCATTTAGCGAAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTa  <  2:121774/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                     
GTGATGCAATAATAGATGAACAAGGTGAGCCACTTAGCGAACAAGTGAATCGTCAAATGATTAAATGGACGAAACTTTATATCGATCAATTTCTATCGAGTTGGACAATGCCGAAGCGTGAGCAAAGTTTTTACCATGCATGGTTGCATTTAGCGCAACATGACCATAGTTTTACTAAAGCACAGCGCCAAGTGATTAAAGGCTTACCCAATGATCCTGAAATGACGATAGAGTCAGTATTAACTCATTTTTCAATAGATCAGGAAGACTA  >  CP000730/479416‑479686

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: ‑