Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,744,362 G→A 11.1% H104Y (CAC→TAC)  apt ← Adenine phosphoribosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,744,3620GA11.1% 137.6 / 7.5 54H104Y (CAC→TAC) aptAdenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base A (3/3);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.87e-01

ATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCG  >  USA300TCH1516_ALE/1744229‑1744502
                                                                                                                                     |                                                                                                                                            
attATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGtt                                                                                                                                       >  1:446324/1‑141 (MQ=255)
attATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACAAACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGtt                                                                                                                                       <  2:420608/141‑1 (MQ=255)
   ataAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACAGGTTGACCTGGTTTAATTGCATCTTTGTGCTTTGTTaaa                                                                                                                                    >  1:895/1‑141 (MQ=255)
        tGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTATTTTAGAGACAATGATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACAtt                                                                                                                               >  1:557474/1‑141 (MQ=255)
          cactACCGACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTg                                                                                                                             <  1:63236/138‑1 (MQ=255)
          cAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACAttgg                                                                                                                             >  2:687304/1‑139 (MQ=255)
          cAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTg                                                                                                                             <  2:442905/141‑1 (MQ=255)
            aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTGAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGtc                                                                                                                           >  1:526242/1‑140 (MQ=255)
            aTACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTGATTGCATCTTTGTGCATTCTTAAAACATTTGTa                                                                                                                           >  1:264199/1‑141 (MQ=255)
              aCCTACTACGATACCGCCTAATTTTGCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTAcc                                                                                                                         <  1:636467/141‑1 (MQ=255)
                 tactacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAAGACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCata                                                                                                                      >  2:445282/1‑141 (MQ=255)
                  actacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCGATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACAAACGTTGACCTGGTTTAATTACATCTTTGTGCATTGTTAAAACATTTGTACCatat                                                                                                                     >  2:483468/1‑141 (MQ=255)
                        aTACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTATCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAgg                                                                                                               <  2:14743/141‑1 (MQ=255)
                        aTACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAgg                                                                                                               >  1:185503/1‑141 (MQ=255)
                         tACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGt                                                                                                              >  2:656157/1‑141 (MQ=255)
                                tAATTGTTCAACTAATTTTATTGCTGCTCCAATCGTACCACCAGTAGCTAATAAATTATCTGTAATTAACACACGTTTACCTTGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCGAGGTCATACTc                                                                                                       <  2:253525/141‑1 (MQ=255)
                                 aaTTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCa                                                                                                      >  2:67742/1‑141 (MQ=255)
                                        cAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGaa                                                                                               <  1:484976/141‑1 (MQ=255)
                                        cAACTAATTTTATTGCTGCCTAAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGaa                                                                                               >  1:758861/1‑141 (MQ=255)
                                         aaCTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAAt                                                                                              <  2:297813/141‑1 (MQ=255)
                                          aCTAATTTTATTGCTGCTTCAATCGTACCACCAGGAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATg                                                                                             <  2:89902/141‑1 (MQ=255)
                                              aTTTTAGTGCGGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACtt                                                                                         <  1:68413/141‑1 (MQ=255)
                                                      gctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGt                                                                                 <  1:752722/141‑1 (MQ=255)
                                                            tCAATCGTACCACCAGTAGCGAATAAATCATCCGTCCCTTACACGCGTTGACGTACCTTAATTGCATATTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATCACTTCACGCGGTAATTTc                                                                           >  1:181292/1‑141 (MQ=255)
                                                             cAATCGTACCACCATTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                          <  1:53978/141‑1 (MQ=255)
                                                             cAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTTTCGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                          <  1:369953/141‑1 (MQ=255)
                                                             cAACCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTcc                                                                          <  1:54044/141‑1 (MQ=255)
                                                                tCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAAGTAATTTCCctt                                                                       >  1:660136/1‑141 (MQ=255)
                                                                      caccaGGAGCTAATAAAACATCTGTAATGAACACACGTTTACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTCTTTTc                                                                 <  2:452679/141‑1 (MQ=255)
                                                                       accaGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCAGGCGGTGATTTCCCTTCTTTTCt                                                                >  2:392205/1‑141 (MQ=255)
                                                                          aGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                             <  2:355433/141‑1 (MQ=255)
                                                                           gTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTTATAACGAATGACTTCACGAGGTAATTTTCCTTCTTTTTTAAct                                                            >  1:322574/1‑140 (MQ=255)
                                                                                    aaaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAg                                                   <  2:185503/141‑1 (MQ=255)
                                                                                     aaTCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTCTTTTCTAACAGGTGCAAAGc                                                  >  2:646447/1‑141 (MQ=255)
                                                                                         atcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAAt                                              >  2:707571/1‑141 (MQ=255)
                                                                                             ttAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcccc                                          <  2:423567/140‑1 (MQ=255)
                                                                                             gTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATcccc                                          <  1:209562/141‑1 (MQ=255)
                                                                                              tAATTACCACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                         <  1:343746/141‑1 (MQ=255)
                                                                                              tAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCa                                         <  1:762557/141‑1 (MQ=255)
                                                                                                  tAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGa                                     >  1:628580/1‑141 (MQ=255)
                                                                                                  tAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGa                                     <  1:38570/141‑1 (MQ=255)
                                                                                                    acacacGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAAt                                   >  2:209615/1‑141 (MQ=255)
                                                                                                        acGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                               <  1:401790/141‑1 (MQ=255)
                                                                                                        acGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGc                               <  1:294022/141‑1 (MQ=255)
                                                                                                            tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCACTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACa                           >  1:412464/1‑141 (MQ=255)
                                                                                                            tGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAAGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACa                           <  2:660136/141‑1 (MQ=255)
                                                                                                                  ggTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATAACTTCACGAGGTAATTTCCCTTCTTTTCTACCAGGTGCAAAGCCAATCCCCATTGAATCAGCCACAGGACac                     >  2:577620/1‑140 (MQ=255)
                                                                                                                     ttAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATACTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCCTTGAATAAGCTACAGGACAGCCa                  >  2:3176/1‑141 (MQ=255)
                                                                                                                         ttGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACGGGACAGCCAATGa              >  1:244787/1‑141 (MQ=255)
                                                                                                                          tGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGAt             <  2:182616/141‑1 (MQ=255)
                                                                                                                            cATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTGATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATaa           >  1:645982/1‑141 (MQ=255)
                                                                                                                               cTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGATAAAGc        <  2:47342/141‑1 (MQ=255)
                                                                                                                               cTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGCCAGCCAATAATAAAGc        >  2:236761/1‑141 (MQ=255)
                                                                                                                                 ttGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCa      <  2:446324/141‑1 (MQ=255)
                                                                                                                                  tgtgCATTGTTAACACATTTGTACCATACTCTAGGTCATACTCATAACGGATGACTTCACGAGTTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGTTACAGGACAGCCAATGGTAAAGcacc     >  2:529979/1‑138 (MQ=255)
                                                                                                                                     gCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcgcg  <  1:667276/141‑1 (MQ=255)
                                                                                                                                     |                                                                                                                                            
ATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACGCG  >  USA300TCH1516_ALE/1744229‑1744502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑