Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,797,152 G→A 18.4% S213S (TCC→TCT)  phoR ← Alkaline phosphatase synthesis sensor protein PhoR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,797,1520GA18.4% 84.3 / 12.1 37S213S (TCC→TCT) phoRAlkaline phosphatase synthesis sensor protein PhoR
Reads supporting (aligned to +/- strand):  ref base G (16/14);  new base A (3/4);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 6.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.56e-01

CCGTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAATTGTGTTGC  >  USA300TCH1516_ALE/1797012‑1797292
                                                                                                                                            |                                                                                                                                            
ccGTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTg                                                                                                                                              >  2:419730/1‑141 (MQ=255)
  gTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGa                                                                                                                                            >  1:84936/1‑141 (MQ=255)
      tAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGa                                                                                                                                        <  1:172717/141‑1 (MQ=255)
      tAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGa                                                                                                                                        <  1:172719/141‑1 (MQ=255)
       aGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGaa                                                                                                                                       >  1:296875/1‑141 (MQ=255)
         ccTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAAtt                                                                                                                                     >  2:447611/1‑141 (MQ=255)
         ccTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAAtt                                                                                                                                     >  2:262366/1‑141 (MQ=255)
         ccTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAAtt                                                                                                                                     >  2:255119/1‑141 (MQ=255)
          cTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTCGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAAttt                                                                                                                                    >  2:389839/1‑141 (MQ=255)
                                    ttGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAgg                                                                                                          >  1:183139/1‑141 (MQ=255)
                                      gAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGcg                                                                                                        >  1:386282/1‑141 (MQ=255)
                                       aaCTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGcgt                                                                                                       >  1:242528/1‑141 (MQ=255)
                                         cTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGcgtcg                                                                                                     <  1:139953/141‑1 (MQ=255)
                                         cTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTATTGCTCATTATTAAGCTTTTGAAGGcgtcg                                                                                                     <  2:413484/141‑1 (MQ=255)
                                           gTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTg                                                                                                   <  1:151851/141‑1 (MQ=255)
                                           gTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTg                                                                                                   <  1:315812/141‑1 (MQ=255)
                                           gTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTCTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTg                                                                                                   <  1:233221/141‑1 (MQ=255)
                                                     cGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCAtt                                                                                         >  1:443771/1‑141 (MQ=255)
                                                            tttGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGac                                                                                  >  1:303596/1‑141 (MQ=255)
                                                            tttGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGac                                                                                  >  1:53378/1‑141 (MQ=255)
                                                                caacaaCGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGTCTCaa                                                                              >  2:362870/1‑141 (MQ=255)
                                                                caacaaCGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACaa                                                                              >  1:309934/1‑141 (MQ=255)
                                                                        aTTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCt                                                                      >  1:380872/1‑141 (MQ=255)
                                                                        aTTTTTCCATTTCGATCTATCATTAAAATAGCACTCGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGCGCTAAATCATTGGTAGACACAAAAAACGCt                                                                      >  1:329903/1‑141 (MQ=255)
                                                                         tttttCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCtt                                                                     <  1:154278/141‑1 (MQ=255)
                                                                                   tCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTac                                                           <  2:36558/141‑1 (MQ=255)
                                                                                   tCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGAAACAAAAAGCGCTTTAGTTTCTac                                                           <  2:155816/141‑1 (MQ=255)
                                                                                            cATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACt                                                  <  2:443771/141‑1 (MQ=255)
                                                                                                 aaaTAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAg                                             <  1:262366/141‑1 (MQ=255)
                                                                                                 aaaTAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAg                                             <  1:447611/141‑1 (MQ=255)
                                                                                                 aaaTAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAg                                             <  1:255119/141‑1 (MQ=255)
                                                                                                              aaTATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTAtgtg                                >  1:187617/1‑141 (MQ=255)
                                                                                                               atatTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGa                               >  2:336230/1‑141 (MQ=255)
                                                                                                               atatTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGa                               >  1:26428/1‑141 (MQ=255)
                                                                                                                            ttgttTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTg                  <  2:380872/141‑1 (MQ=255)
                                                                                                                            ttgttATTAAACGGTTAGATTTAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACTCGTATGTGATAATAACCATTTg                  <  2:329903/141‑1 (MQ=255)
                                                                                                                                    aaaCGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATAAGTAAACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAAt          <  2:296875/141‑1 (MQ=255)
                                                                                                                                     aaCGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAAtt         <  1:455110/141‑1 (MQ=255)
                                                                                                                                            ggATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAATTGTGTTGc  <  1:176271/141‑1 (MQ=255)
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CCGTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAATTGTGTTGC  >  USA300TCH1516_ALE/1797012‑1797292

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: ‑