Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,468,118 C→T 8.2% A66T (GCA→ACA)  USA300HOU_1366 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,468,1180CT 8.2% 140.9 / 3.5 49A66T (GCA→ACA) USA300HOU_1366hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (18/27);  new base T (2/2);  total (20/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

TAAAAGTTAATAATTCAGCTTTAATTTCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTAGATAACTTGTCTTCTCTTGTAT  >  CP000730/1467980‑1468252
                                                                                                                                          |                                                                                                                                       
tAAAAGTTAATAATTCAGCTTTAATTTCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCt                                                                                                                                       <  2:407828/141‑1 (MQ=255)
  aaaGTTAATAATTCAGCTTTAATTTCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTa                                                                                                                                     <  1:567442/141‑1 (MQ=255)
  aaaGTTAATAATTCAGCTTTAATTTCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTa                                                                                                                                     <  1:239037/141‑1 (MQ=255)
    aGTTAATAATTCAGCTTTAATTTCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCTGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATc                                                                                                                                   <  1:429551/141‑1 (MQ=255)
          taatTCAGCTTTAATTTCACCAAAATGATGGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGc                                                                                                                             <  2:301309/141‑1 (MQ=255)
               ccgatttAAGTCCAACAAAATGATTGTCACTTTGAGGTTAATGGACAAATCCTTAAACCTGATTCGCATCAGAAAAAGCAGCTTTAATATCCAGTAATAGTACTTCCCTGTCAGCTGTTTGCTCCTTATCAACTGATa‑aga                                                                                                                       <  2:327247/137‑1 (MQ=255)
                 gCTTTAATTTCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTa‑agaag                                                                                                                     <  1:402455/141‑1 (MQ=255)
                         ttCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTcatgac                                                                                                             <  2:79298/141‑1 (MQ=255)
                         ttCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTcatgac                                                                                                             >  1:337895/1‑141 (MQ=255)
                           cACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTcatgacat                                                                                                           <  1:60594/141‑1 (MQ=255)
                            aCCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGTCTTATCAACAGCTA‑AGAAGTTcatgacatg                                                                                                          >  1:610269/1‑141 (MQ=255)
                            aCCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGTCTTATCAACAGCTA‑AGAAGTTcatgacatg                                                                                                          >  1:610388/1‑141 (MQ=255)
                               aaaaTGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGaaa                                                                                                       >  2:52680/1‑141 (MQ=255)
                                aaaTGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGaaaa                                                                                                      >  2:205122/1‑141 (MQ=255)
                                     aTTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACACCGT‑AGTAGTTCATGACATGAAAAATGGa                                                                                                 <  2:40803/141‑1 (MQ=255)
                                        gTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTAATGACATGAAAAATGGAAGt                                                                                              <  1:407470/141‑1 (MQ=255)
                                        gTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCGA‑AGAAGTTCCTGACATGGAAAATGGAAGt                                                                                              <  2:6437/141‑1 (MQ=255)
                                          cAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGa                                                                                            <  2:370692/141‑1 (MQ=255)
                                             tttGATGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTCTCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATAc                                                                                         <  1:129666/141‑1 (MQ=255)
                                              ttGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGAGATGAAAAAGGGAAGTGATAcc                                                                                        <  1:347405/141‑1 (MQ=255)
                                               tGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCa                                                                                       <  2:347200/141‑1 (MQ=255)
                                                 aGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCAta                                                                                     >  1:640284/1‑140 (MQ=255)
                                                 aGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATc                                                                                     <  2:392116/141‑1 (MQ=255)
                                                                           tATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTTCCTTATCAACAGCTA‑ATAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATc                                                           <  2:595630/141‑1 (MQ=255)
                                                                            aTTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATAACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGCAAGTGATACGATCTATAGATACCATCTCAtttctcattct                                                          >  1:205/1‑133 (MQ=255)
                                                                               cGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTgg                                                       >  1:25488/1‑141 (MQ=255)
                                                                                 cATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTgggg                                                     >  2:465535/1‑139 (MQ=255)
                                                                                  aTCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTAGCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTtg                                                    <  1:613513/141‑1 (MQ=255)
                                                                                     aGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTgtgt                                                 <  1:541027/141‑1 (MQ=255)
                                                                                      gAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGtt                                                >  1:83383/1‑141 (MQ=255)
                                                                                           agcagcTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTttcttt                                           >  1:234375/1‑140 (MQ=255)
                                                                                           agcagcTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTttcttc                                           >  1:161257/1‑141 (MQ=255)
                                                                                           agcagcTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTttcttc                                           >  1:529247/1‑141 (MQ=255)
                                                                                            gcagcTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTtcttct                                          <  2:476340/141‑1 (MQ=255)
                                                                                            gcagcTTTAATATCAGGTAATATGACCACCCAACCAGCCTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTtcttct                                          <  1:346541/141‑1 (MQ=255)
                                                                                                cTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGTCTTATCAACAGCTA‑AGAAGTTCATGACATGGAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACtt                                      <  2:610269/141‑1 (MQ=255)
                                                                                                cTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGTCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACtt                                      <  2:610388/141‑1 (MQ=255)
                                                                                                    gatttCAGGTTATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGATA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACtttttt                                  <  2:552914/137‑1 (MQ=255)
                                                                                                    aaTATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACtttttt                                  <  2:407834/141‑1 (MQ=255)
                                                                                                           ggTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTa                           <  1:435078/141‑1 (MQ=255)
                                                                                                             tAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTAtt                         >  2:70297/1‑141 (MQ=255)
                                                                                                             tAATATGACTTCCCAATCAGCTTTTGGTGCCTTATC‑GCGGCGAGGGAAGATCGCCACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATACGTAtt                         >  1:157293/1‑141 (MQ=255)
                                                                                                                 atGACTTCCCGATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTAGAt                     >  1:484020/1‑141 (MQ=255)
                                                                                                                    aCTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTGCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTAGATAAc                  >  1:130422/1‑141 (MQ=255)
                                                                                                                        cccAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTAGATAACTTGt              <  1:11936/141‑1 (MQ=255)
                                                                                                                          cAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGGTACCATCTATAGATACCAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTGGATAAGTTGtgt            >  1:271885/1‑139 (MQ=255)
                                                                                                                          cAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTAGATAACTTGtct            <  1:298008/141‑1 (MQ=255)
                                                                                                                                  ttttGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCGATAGATAACAACTGATTTATAAATCTCGGTGCTGTTTCTTATACTTTTTTATAAGTATTAGATAACTTGTCTTCTCTTGt    >  1:253610/1‑141 (MQ=255)
                                                                                                                                    ttGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTAGATAACTTATATTATCTTGtat  >  2:372702/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                                       
TAAAAGTTAATAATTCAGCTTTAATTTCACCAAAATGATTGTCAATTTGAGGTTCATTTACAGATTCTAAAACCTTATTCGCATCAGAAAAAGCAGCTTTAATATCAGGTAATATGACTTCCCAATCAGCTTTTGGTGCCTTATCAACAGCTA‑AGAAGTTCATGACATGAAAAATGGAAGTGATACCATCTATAGATAACAACTGATTTATAAATCTTGGTTGTGTTTCTTCTACTTTTTTATAAGTATTAGATAACTTGTCTTCTCTTGTAT  >  CP000730/1467980‑1468252

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑