Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,124,5130TG22.7% 97.2 / 11.2 44L214R (CTA→CGA) USA300HOU_2004possible bifunctional S24 family peptidase/transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (12/22);  new base G (0/10);  total (12/32)
Fisher's exact test for biased strand distribution p-value = 4.11e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TATGGAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTATGAATGAACATATG  >  CP000730/2124364‑2124655
                                                                                                                                                     |                                                                                                                                              
tATGGAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACta                                                                                                                                               <  1:53837/151‑1 (MQ=255)
tATGGAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACta                                                                                                                                               >  1:304388/1‑151 (MQ=255)
   ggAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGCAAACGCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACtaaat                                                                                                                                            >  2:846554/1‑151 (MQ=255)
        cTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGa                                                                                                                                       <  1:321251/151‑1 (MQ=255)
        cTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGa                                                                                                                                       <  2:79744/151‑1 (MQ=255)
        cTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGa                                                                                                                                       <  1:467265/151‑1 (MQ=255)
          aTGTTTAAAGATGGCGAAATCATTTTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCGTTGTTGAAGTTGATAGATTGACGCTAGTTTCACTATATAAAGAtt                                                                                                                                     <  1:480120/151‑1 (MQ=255)
           tGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTa                                                                                                                                    <  1:680344/151‑1 (MQ=255)
            gTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTac                                                                                                                                   <  2:769669/151‑1 (MQ=255)
                       gCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTaca                                                                                                                        >  2:72691/1‑151 (MQ=255)
                       gCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTaca                                                                                                                        >  1:918264/1‑151 (MQ=255)
                           aaTCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCATTGTTGAAGATGATAGATTGACACTAGTTTCACTAAATAAAGATTACGACGATCTACACttt                                                                                                                    <  1:174181/151‑1 (MQ=255)
                            aTCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACtttt                                                                                                                   <  1:601015/151‑1 (MQ=255)
                                         agaAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAg                                                                                                      <  1:507378/151‑1 (MQ=255)
                                             aaCTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGtgtg                                                                                                  <  1:1044984/151‑1 (MQ=255)
                                              aCTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGa                                                                                                 >  1:438046/1‑151 (MQ=255)
                                               cTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACACTTTTATAGAAATGAAAGTGTGAg                                                                                                <  2:984146/151‑1 (MQ=255)
                                                tCACAATATAAAGAATGGACAAATTGGTATATTTATCATTGAAGAAGAAGCGTACGTTAAGTAAGTCTTTGTTGAAGATGATAGATTTTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACACTTTTATAGAAATGAAAgtgtagat                                                                                               <  2:119501/151‑5 (MQ=255)
                                                 cacaATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGt                                                                                              >  1:499019/1‑151 (MQ=255)
                                                 cacaATATAAAAAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGt                                                                                              <  1:744527/151‑1 (MQ=255)
                                                     atatAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAAt                                                                                          >  1:153030/1‑151 (MQ=255)
                                                      tataACGACTGGACCAATTGGTATATTCATCATTGAAGAAGAAGCTTACTTTAAGTAAGTCTTTGTTGAAGATGATAGATTGTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAAtt                                                                                         <  2:1052353/151‑1 (MQ=255)
                                                             aaTGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAg                                                                                  <  1:878046/151‑1 (MQ=255)
                                                              aTGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGt                                                                                 >  1:633556/1‑151 (MQ=255)
                                                                         ggTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATaaa                                                                      >  2:961611/1‑151 (MQ=255)
                                                                           tataTTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAg                                                                    <  2:818045/151‑1 (MQ=255)
                                                                            atatTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGTCTTTTTTTTAATGATACAGAGATTACCGAGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAgg                                                                   <  2:90319/151‑1 (MQ=255)
                                                                              atTCATCATTGAAGAAGAAGCGTACGTTAAGAGAGTCTTTGTTGAAGATGATAGATTGTTTTTTTTTTAATGATACGGCGACCACCGAGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAg                                                                 <  2:667628/151‑1 (MQ=255)
                                                                              atTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGTTTTTTTTTTAATGATACGGAGACCACCGAGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAg                                                                 <  2:871160/151‑1 (MQ=255)
                                                                              atTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGGTTTTGTTTAAGATTATATGTTGACTTGATTTTGACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAg                                                                 <  1:423605/151‑1 (MQ=255)
                                                                                 catcatTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGTCTTTATTTTAATGAAACAGAGACTACGGAGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCAc                                                              <  2:613493/151‑1 (MQ=255)
                                                                                  atcatTTAAGAAGAAGCGTACGTTAAGTAAGTCTTTGTTGAAGATGATAGATTGTTTTTTTTTTAATGATACGGCGACCACGGAGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACt                                                             <  2:703502/151‑1 (MQ=255)
                                                                                  atcatTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACt                                                             <  1:961611/151‑1 (MQ=255)
                                                                                  atcatTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACt                                                             <  1:573402/151‑1 (MQ=255)
                                                                                                    tACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAatatt                                           <  1:622104/151‑2 (MQ=255)
                                                                                                      cGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGat                                         >  2:53808/1‑151 (MQ=255)
                                                                                                                 tCTTTGTTGAAGATGATAGATTGTCTCTTGTTTCACGAAACAAAGACCACCGCGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCtt                              <  2:304388/151‑1 (MQ=255)
                                                                                                                  cTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTa                             >  2:549792/1‑151 (MQ=255)
                                                                                                                     tgttgAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGAc                          <  1:41180/151‑1 (MQ=255)
                                                                                                                      gttgAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACt                         <  1:846554/151‑1 (MQ=255)
                                                                                                                        tgAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACttt                       <  1:438185/151‑1 (MQ=255)
                                                                                                                        tgAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACttt                       >  1:751709/1‑151 (MQ=255)
                                                                                                                        tgAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACttt                       >  1:48452/1‑151 (MQ=255)
                                                                                                                                 tAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTatg              <  1:940153/151‑1 (MQ=255)
                                                                                                                                  aGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTatga             <  1:53808/151‑1 (MQ=255)
                                                                                                                                       gACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTAtgaatgaa        <  1:85840/151‑1 (MQ=255)
                                                                                                                                             aGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTATGAATGAACATATg  >  2:244216/1‑151 (MQ=255)
                                                                                                                                                     |                                                                                                                                              
TATGGAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTATGAATGAACATATG  >  CP000730/2124364‑2124655

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