Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,744,362 G→A 19.0% H104Y (CAC→TAC)  apt ← Adenine phosphoribosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,744,3620GA19.0% 100.8 / 22.5 54H104Y (CAC→TAC) aptAdenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base G (17/26);  new base A (5/5);  total (22/32)
Fisher's exact test for biased strand distribution p-value = 7.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.27e-01

TATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACG  >  USA300TCH1516_ALE/1744231‑1744500
                                                                                                                                   |                                                                                                                                          
tataAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTaa                                                                                                                                   >  2:542485/1‑141 (MQ=255)
  taAATGCAATACCTACTACCATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTaaaa                                                                                                                                 <  1:485213/141‑1 (MQ=255)
   aaaTGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAAc                                                                                                                                >  2:103427/1‑141 (MQ=255)
          aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTa                                                                                                                         >  2:226772/1‑141 (MQ=255)
          aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTa                                                                                                                         <  1:547114/141‑1 (MQ=255)
              ctactaCGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCat                                                                                                                     <  1:155019/141‑1 (MQ=255)
                 ctacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCTTAtt                                                                                                                  <  2:422881/141‑1 (MQ=255)
                   acaaaaCCGCCTAATCTTTCAACTAAACATATTGCCGCTCCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCt                                                                                                                <  1:182607/136‑1 (MQ=255)
                     gATACCGCCTAATTTTTCAACTAATTCTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAATACATTTGTACCATATTCTAg                                                                                                              <  1:371331/141‑1 (MQ=255)
                       tACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTTAAACATTTGTACCATATTCTAGGt                                                                                                            <  1:446365/141‑1 (MQ=255)
                       tACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACCTTTATTTTTTTTAATTGCATCTTTGTGCATTGTTTAAACATTTGTACCATATTCTAGGt                                                                                                            <  1:446465/141‑1 (MQ=255)
                        aCCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTc                                                                                                           <  1:88511/141‑1 (MQ=255)
                         cccccTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                          <  2:59362/138‑1 (MQ=255)
                         ccGCCTAATTTTTCAACTAATTTTATTGATGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                          >  1:448992/1‑141 (MQ=255)
                          cGCCGAATTTTTCAACTACTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTTACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCAt                                                                                                         <  1:510520/141‑1 (MQ=255)
                                 tttttCAATTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGCTTAATTGCATCTTTGTGCATTGCTAAAACATTTGTACCATATTCTAGGTCATACTCAtt                                                                                                  <  2:145446/141‑2 (MQ=255)
                                     tCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATGCTCATAACGa                                                                                              >  2:89948/1‑141 (MQ=255)
                                      cAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTTCATCTTTGTGCATTGTTAAAACATTTGTCCCATATTCTAGGTCATCATCATAACGaa                                                                                             >  1:45766/1‑141 (MQ=255)
                                        aCTAATTTTATTGCTGTTTCAATCGTACCATTATTATCTAATAATTCATCTGTAATTAACATACGTTGACCTGTTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGTTCATACTCATAACGAATg                                                                                           <  2:60310/141‑1 (MQ=255)
                                          tAATTTTATTCCTCCTTCAATCGTACCACCAGTAGCTAATAAATCATCAGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGAc                                                                                         <  2:147501/141‑1 (MQ=255)
                                           aactttATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACt                                                                                        <  2:441928/138‑1 (MQ=255)
                                           aaTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTTTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACt                                                                                        >  1:501079/1‑141 (MQ=255)
                                                 aTTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGa                                                                                  <  1:103427/141‑1 (MQ=255)
                                                 aTTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGa                                                                                  >  2:57618/1‑141 (MQ=255)
                                                      tgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTaa                                                                             >  2:187224/1‑141 (MQ=255)
                                                          tCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTc                                                                         <  1:355631/141‑1 (MQ=255)
                                                           cactCGTACCACCTGTAGCTTATAATTCATCTGTTATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                        <  1:5596/138‑1 (MQ=255)
                                                           cAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                        <  2:508378/141‑1 (MQ=255)
                                                           cAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                        <  1:511883/141‑1 (MQ=255)
                                                            aaTCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTccc                                                                       <  2:104784/141‑1 (MQ=255)
                                                              tCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCctt                                                                     >  2:297288/1‑141 (MQ=255)
                                                                  accaccAGTAGCTAATAAATCATCTGTAAGTAACACACGTTGACCTGGTTTAATTGAATCTTTGTACATTGTTAAAACATTTGTACAATAATCTAGTTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCttt                                                                 >  2:398746/1‑141 (MQ=255)
                                                                    caccaGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATACCGCAAGACTTCACGAGGGACCTTACCTTCTTTTc                                                               >  2:263577/1‑141 (MQ=255)
                                                                       caGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTaa                                                            >  2:285697/1‑141 (MQ=255)
                                                                        attAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                           <  2:263082/139‑1 (MQ=255)
                                                                        aGTAGCTAATAAATCATCTGTTATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                           <  2:596050/141‑1 (MQ=255)
                                                                        aGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                           <  1:179976/141‑1 (MQ=255)
                                                                               aataaATCATCTGTAAATAAGACATGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGGAATTTCCCTTCTTTTCTAACAGTTGCa                                                    >  2:282233/1‑141 (MQ=255)
                                                                                ataaATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGATGCaa                                                   >  1:131065/1‑141 (MQ=255)
                                                                                  aaaTCATCTTTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTCCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACGTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAg                                                 <  2:99367/141‑1 (MQ=255)
                                                                                      cagcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCaa                                             <  1:259000/138‑1 (MQ=255)
                                                                                          tGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATccc                                         >  1:557830/1‑141 (MQ=255)
                                                                                            tAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                       <  2:607926/141‑1 (MQ=255)
                                                                                                 aaCACACGTTTACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGaa                                  <  2:592928/141‑1 (MQ=255)
                                                                                                  acacacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTCCCCTATTCTCGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGTCAATCCAATCCCCATTGAAt                                 >  1:210924/1‑141 (MQ=255)
                                                                                                      acGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTACAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                             <  1:397982/141‑1 (MQ=255)
                                                                                                      acGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                             <  2:195125/141‑1 (MQ=255)
                                                                                                          tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATTACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACa                         >  1:189792/1‑141 (MQ=255)
                                                                                                             ccTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACTATATTCTAGGTCATCCTCATAGCGAATGACTTAACGAGGTTATTTTCCTTCTTTTCTAACAGGTGGAAAGGCATTATCCATAGAATTAGTTACAGGa                      >  2:846/1‑141 (MQ=255)
                                                                                                               tGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACa                    >  1:522033/1‑141 (MQ=255)
                                                                                                                  tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGcc                 >  2:85268/1‑141 (MQ=255)
                                                                                                                  tttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGcc                 >  2:103678/1‑141 (MQ=255)
                                                                                                                     aatgtcATCTTTGTGCATTGTTAAAACATTTGTACCAGATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAAt              <  2:548808/136‑1 (MQ=255)
                                                                                                                              tttGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGcc     <  2:494620/141‑1 (MQ=255)
                                                                                                                                tgtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCAc   >  1:309060/1‑141 (MQ=255)
                                                                                                                                 gtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGCCAcg  >  1:160001/1‑141 (MQ=255)
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TATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACG  >  USA300TCH1516_ALE/1744231‑1744500

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: ‑