Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,027,694 A→T 14.4% S85T (TCA→ACA)  vraS ← Sensor protein VraS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,027,6940AT14.4% 100.3 / 14.4 49S85T (TCA→ACA) vraSSensor protein VraS
Reads supporting (aligned to +/- strand):  ref base A (20/22);  new base T (2/5);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.58e-02

TGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAAC  >  USA300TCH1516_ALE/2027559‑2027833
                                                                                                                                       |                                                                                                                                           
tGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTGAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTATGATCATTAATGCCAACTGTGTCGGCTTCCATTGaaattt                                                                                                                                        >  2:526168/1‑137 (MQ=255)
  gTTAAGATTTGAGTTTTAAGTCGCCAATTATGCAATTCTTGCCTTAAAGGTACAAGTGTATGGTATAAGAATTACGATTCACTATAAATTTCTATATTTTGATCATTAATGCCAAATGTTTCGCCTTCCATTGAACGCTCa                                                                                                                                      >  2:201831/1‑141 (MQ=255)
          ttGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGt                                                                                                                              <  1:191098/141‑1 (MQ=255)
           tGAGTTTTAAATCGCAACTTATGCAATTCTTGACTAAAAGGTAAAAGGGTATGGTGGATAGCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGCTTCGCCTTCCATTTAACGCTCAATTTACgcc                                                                                                                             >  2:585497/1‑139 (MQ=255)
            gAGTTTTAAGTCGCAACTTATGCAATTCTTGGTTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCCTTGAACGCTCAATTTGCATCt                                                                                                                            >  2:360495/1‑141 (MQ=255)
                   aaGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGTCTTAATCCa                                                                                                                     <  1:36481/141‑1 (MQ=255)
                        gCAACTTATGCAGTTCTTGATGTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCAt                                                                                                                >  1:317064/1‑141 (MQ=255)
                        gCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCAt                                                                                                                <  1:36296/141‑1 (MQ=255)
                                       cTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGAttt                                                                                                 <  1:509593/141‑1 (MQ=255)
                                               aaaGGTACAAGTGACTGGTTTACATATAACGTTTCACTATATATTTCTATATGTTGATAATTAATGCCAAATAGATTGCCTACGATTGAACGGTCAATTTCCGTCTTAATCCAATCATTGTGAGGATTGATTTTGTAAGCg                                                                                         >  2:283485/1‑141 (MQ=255)
                                                aaGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTCTGCTGATTGATTTTGTAAGCGa                                                                                        >  2:566339/1‑141 (MQ=255)
                                                 aGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAg                                                                                       >  1:127795/1‑141 (MQ=255)
                                                   gTACACGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCCACTGTTTCGCCTGCCATTGAACGCTCAATTTGCGTCGTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTa                                                                                     <  2:99735/141‑1 (MQ=255)
                                                   gTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTa                                                                                     <  1:529311/141‑1 (MQ=255)
                                                   gTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTATTAATCAAATCATTTTGCTGATTGATTTTGTaacgtagtc                                                                                     >  2:70972/1‑134 (MQ=255)
                                                          tgtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAAcc                                                                              >  2:534058/1‑141 (MQ=255)
                                                          tgtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAAcc                                                                              <  2:553536/141‑1 (MQ=255)
                                                            tATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAACGAGTACCGAACcaa                                                                            >  1:281438/1‑141 (MQ=255)
                                                                gTATAAATCTAACGTTTCACTATATCTTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACaat                                                                        <  2:412126/141‑1 (MQ=255)
                                                                gTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACaat                                                                        <  1:374841/141‑1 (MQ=255)
                                                                gTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACcaacaaa                                                                        >  2:96255/1‑140 (MQ=255)
                                                                        cTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCAGTGAACGCTCAATTTGCGTCTTAAACCAATCATTTTGATGATTGATTTTGTAAGCGAGTACCGCAGCATCaatattccaga                                                                >  2:300683/1‑134 (MQ=255)
                                                                         tAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACaa                                                               <  1:506688/141‑1 (MQ=255)
                                                                          aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACATTAATACACaaa                                                              >  1:469659/1‑140 (MQ=255)
                                                                              gttCACTATATAGTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCTAACCAACAATAATACACAataata                                                          >  2:383058/2‑141 (MQ=255)
                                                                                tCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatg                                                        <  1:127704/141‑1 (MQ=255)
                                                                                  aCTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGAACAGATCCATCATTACTATACAATAATatgat                                                      >  1:594866/1‑141 (MQ=255)
                                                                                    tatattTTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgatga                                                    <  2:148627/141‑1 (MQ=255)
                                                                                     atatatTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgatgat                                                   <  1:114067/141‑1 (MQ=255)
                                                                                     atatatTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgatgat                                                   <  2:595616/141‑1 (MQ=255)
                                                                                     atatagTTCCATATTTTGCTCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCCAATTTCGCCGTATTCCAATTTTTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgatgat                                                   <  2:65918/141‑1 (MQ=255)
                                                                                       atatTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACAAAGAAGAAGTCACAATAATAtgatgatga                                                 <  1:449699/141‑1 (MQ=255)
                                                                                            tCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAttt                                            <  1:300588/141‑1 (MQ=255)
                                                                                               atatTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGTACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCGACAATAATACACAATAATATGATGATGAGATTtaaa                                         >  1:152766/1‑141 (MQ=255)
                                                                                                tatTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaa                                        <  1:437368/141‑1 (MQ=255)
                                                                                                tatTTTGATCATGAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaa                                        <  1:360495/141‑1 (MQ=255)
                                                                                                     tGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAGTTGGCGTCTGAATCCAATCAAGTGGCTGATTGATTTTGTAAGCGCGTACCGAACCAACAATAATACACAATAATATGATGATGACATTtaaaaataaa                                   >  2:100779/1‑141 (MQ=255)
                                                                                                      gATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTtaaaaataaaa                                  >  2:274583/1‑141 (MQ=255)
                                                                                                           ttAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACt                             >  2:67203/1‑141 (MQ=255)
                                                                                                             aaTGCCAACTGTTTCGCCTTCCATTGAACGCGCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTgg                           <  1:218816/141‑1 (MQ=255)
                                                                                                                gCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTAt                        <  1:469966/141‑1 (MQ=255)
                                                                                                                    aCTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCg                    <  1:459925/141‑1 (MQ=255)
                                                                                                                    aCTGTTTCGCCTTCCATTGAACGCTCAATTTGAGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCg                    <  1:41799/141‑1 (MQ=255)
                                                                                                                         ttggCCTTCAATTGTACGCTCAATGTGCGTTTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGATTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAatat               <  2:94969/138‑1 (MQ=255)
                                                                                                                            gCCTTTCATTGAACGCTCAATTTGCGTATTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACTCAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtg            <  2:142946/141‑1 (MQ=255)
                                                                                                                            gCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtg            >  1:171147/1‑141 (MQ=255)
                                                                                                                            gCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTACGAATATTtg            >  2:534958/1‑141 (MQ=255)
                                                                                                                             ccTTCCATTGAACGGTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtgt           <  2:423286/141‑1 (MQ=255)
                                                                                                                             ccTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtgt           >  1:392762/1‑141 (MQ=255)
                                                                                                                             ccTTCCATTGAACGCTCAATTTGCGTCTTAATCAAATCATTTTTCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATTATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTtgt           <  2:469457/141‑1 (MQ=255)
                                                                                                                                      taaCGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATGTTGTAAGCGAGTACCGAACCAACAATAATACACCATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAAc  <  2:317064/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                           
TGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGGTATTCCGAATATTTGTGTATAAAAC  >  USA300TCH1516_ALE/2027559‑2027833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑