Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,124,5170TC22.7% 105.0 / 11.2 44N215N (AAT→AAC) USA300HOU_2004possible bifunctional S24 family peptidase/transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (12/22);  new base C (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.

GGAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTATGAATGAACATATGAACAGCCCTTG  >  CP000730/2124367‑2124666
                                                                                                                                                      |                                                                                                                                                     
ggAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGCAAACGCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACtaaat                                                                                                                                                       >  2:846554/1‑151 (MQ=255)
     cTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGa                                                                                                                                                  <  1:467265/151‑1 (MQ=255)
     cTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGa                                                                                                                                                  <  1:321251/151‑1 (MQ=255)
     cTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGa                                                                                                                                                  <  2:79744/151‑1 (MQ=255)
       aTGTTTAAAGATGGCGAAATCATTTTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCGTTGTTGAAGTTGATAGATTGACGCTAGTTTCACTATATAAAGAtt                                                                                                                                                <  1:480120/151‑1 (MQ=255)
        tGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTa                                                                                                                                               <  1:680344/151‑1 (MQ=255)
         gTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTac                                                                                                                                              <  2:769669/151‑1 (MQ=255)
                    gCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTaca                                                                                                                                   >  1:918264/1‑151 (MQ=255)
                    gCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTaca                                                                                                                                   >  2:72691/1‑151 (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                                                                        <  1:573402/151‑1 (MQ=255)
                                                                               atcatTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACt                                                                        <  1:961611/151‑1 (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                                  >  1:48452/1‑151 (MQ=255)
                                                                                                                     tgAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACttt                                  >  1:751709/1‑151 (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)
                                                                                                                                                     ataaaGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTATGAATGAACATATGAACAGCCCTTg  <  1:545211/151‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                                     
GGAACCTATGTTTAAAGATGGCGAAATCATATTTGTGGAGAAAACTCACAATATAAAGAATGGACAAATTGGTATATTCATCATTGAAGAAGAAGCGTACGTTAAGAAAGTCTTTGTTGAAGATGATAGATTGACTCTAGTTTCACTAAATAAAGATTACGACGATCTACACTTTTATAGAAATGAAAGTGTGAGGTTAATTGGAAAAGTTATTTTATAAAAGGAGCACTTGCAAATGAAAAAATATGATATTGCAGTCTTAGACTTTGAAACTATGAATGAACATATGAACAGCCCTTG  >  CP000730/2124367‑2124666

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑