Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,797,7720GC22.0% 119.5 / 33.5 50R7G (CGC→GGC) phoRAlkaline phosphatase synthesis sensor protein PhoR
Reads supporting (aligned to +/- strand):  ref base G (20/19);  new base C (7/4);  total (27/23)
Fisher's exact test for biased strand distribution p-value = 5.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.03e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAATAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  USA300TCH1516_ALE/1797633‑1797908
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aaataaatATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCgg                                                                                                                                         <  1:60726/141‑1 (MQ=255)
    aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCggtggt                                                                                                                                     <  1:927514/141‑1 (MQ=255)
       tatatGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGaa                                                                                                                                  <  1:443525/141‑1 (MQ=255)
        atatGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGaaa                                                                                                                                 >  1:383729/1‑141 (MQ=255)
        atatGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGaaa                                                                                                                                 >  1:383743/1‑141 (MQ=255)
            gATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATTTGTGATGAAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTtc                                                                                                                             <  2:226761/141‑1 (MQ=255)
             aTCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTtca                                                                                                                            <  1:61984/141‑1 (MQ=255)
             aTCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtca                                                                                                                            >  1:22802/1‑141 (MQ=255)
                 tGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTcatcat                                                                                                                        <  2:174063/141‑1 (MQ=255)
                  gCATCTGTGGCTAGAGCTTGTTCTTTTTTTTCTGAGAAAACACGTGCGAGGTATTCTTGAATAATGATGCCTA‑‑ATGTATCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                       <  1:736592/141‑1 (MQ=255)
                    aTCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGt                                                                                                                     <  1:624420/141‑1 (MQ=255)
                         ttGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTTTTCttt                                                                                                                >  1:94633/1‑141 (MQ=255)
                            cTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAgg                                                                                                             >  1:242601/1‑141 (MQ=255)
                             tAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGt                                                                                                            <  1:644952/141‑1 (MQ=255)
                               gagCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCt                                                                                                          <  1:639162/141‑1 (MQ=255)
                                agCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCtt                                                                                                         <  1:47995/141‑1 (MQ=255)
                                  cTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTc                                                                                                       <  1:362775/141‑1 (MQ=255)
                                   ttGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATATGTAACAATACTGATAATTAATATACTGCTTATCAATATCATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCttt                                                                                                        <  1:101497/141‑1 (MQ=255)
                                   ttGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTcc                                                                                                      <  1:132324/141‑1 (MQ=255)
                                    tGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCATGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCa                                                                                                     <  1:139307/141‑1 (MQ=255)
                                     gTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGAGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCaa                                                                                                    <  1:894501/141‑1 (MQ=255)
                                       tCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCACtt                                                                                                  >  1:280057/1‑141 (MQ=255)
                                        cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAttt                                                                                                 >  1:440131/1‑141 (MQ=255)
                                              tttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGcc                                                                                           >  2:279473/1‑141 (MQ=255)
                                                         aCATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGca                                                                                >  2:261050/1‑141 (MQ=255)
                                                           atatGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGcaca                                                                              <  1:896704/141‑1 (MQ=255)
                                                             atGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGt                                                                            >  1:29345/1‑141 (MQ=255)
                                                              tgtgATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCCATTTATAGCCTAAGCCACGCACAGtt                                                                           >  2:41873/1‑141 (MQ=255)
                                                                 gATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTta                                                                        <  1:781334/141‑1 (MQ=255)
                                                                 gATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTta                                                                        <  2:330075/141‑1 (MQ=255)
                                                                 gATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTta                                                                        >  2:162455/1‑141 (MQ=255)
                                                                    ggAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaata                                                                     >  1:206650/1‑141 (MQ=255)
                                                                          gTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGTTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtgt                                                               <  2:34036/141‑1 (MQ=255)
                                                                            gAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTgg                                                             <  1:182877/141‑1 (MQ=255)
                                                                                  taatGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttctt                                                       >  2:241615/1‑141 (MQ=255)
                                                                                      gCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGa                                                   <  1:848828/141‑1 (MQ=255)
                                                                                        cTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAtt                                                 <  1:610579/141‑1 (MQ=255)
                                                                                        cTA‑‑ATGTAAAAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAtt                                                 >  1:870118/1‑141 (MQ=255)
                                                                                         tA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTa                                                >  1:873288/1‑141 (MQ=255)
                                                                                         tA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTa                                                >  1:561280/1‑141 (MQ=255)
                                                                                                   cAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTaa                                        <  1:251191/141‑1 (MQ=255)
                                                                                                      aaCTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAAttt                                     >  1:696661/1‑141 (MQ=255)
                                                                                                         tGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtc                                  >  1:454860/1‑141 (MQ=255)
                                                                                                          gATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtct                                 >  1:41178/1‑141 (MQ=255)
                                                                                                                  atatACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATg                         <  1:343032/141‑1 (MQ=255)
                                                                                                                       cTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGa                    >  2:71898/1‑141 (MQ=255)
                                                                                                                                 aTAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATATTCTAATCTATCTCTTAAATGACTGATATGTACATc          >  2:187868/1‑141 (MQ=255)
                                                                                                                                      aTTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATcaacaa     >  1:589309/1‑141 (MQ=255)
                                                                                                                                      aTTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATaaacaa     >  1:779533/1‑141 (MQ=255)
                                                                                                                                        tAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAAtt   >  1:826555/1‑141 (MQ=255)
                                                                                                                                         aaGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  >  2:195733/1‑141 (MQ=255)
                                                                                                                                         aaGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  >  2:410780/1‑141 (MQ=255)
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AAATAAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTA‑‑ATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  USA300TCH1516_ALE/1797633‑1797908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑