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

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,744,3620GA83.9% 142.3 / 18.5 56H104Y (CAC→TAC) aptAdenine phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base G (6/3);  new base A (25/22);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 7.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

AATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACG  >  USA300TCH1516_ALE/1744228‑1744500
                                                                                                                                      |                                                                                                                                          
aattATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGt                                                                                                                                      >  2:56210/1‑141 (MQ=255)
  ttATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTa                                                                                                                                    <  2:318263/141‑1 (MQ=255)
    ataAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTaaa                                                                                                                                  >  2:9964/1‑141 (MQ=255)
         tGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACAtt                                                                                                                             >  1:932474/1‑141 (MQ=255)
               aCCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTAcc                                                                                                                       <  2:64186/141‑1 (MQ=255)
                  tactacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCata                                                                                                                    >  1:418668/1‑141 (MQ=255)
                    ctacGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATAtt                                                                                                                  >  1:221745/1‑141 (MQ=255)
                      acGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCt                                                                                                                <  2:319682/141‑1 (MQ=255)
                            ccGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                          >  1:792597/1‑141 (MQ=255)
                            ccGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCa                                                                                                          <  1:153717/141‑1 (MQ=255)
                              gCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATa                                                                                                        >  1:579500/1‑141 (MQ=255)
                               ccTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATAc                                                                                                       <  1:622432/141‑1 (MQ=255)
                                cTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACt                                                                                                      <  1:931427/141‑1 (MQ=255)
                                cTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACt                                                                                                      <  1:359238/141‑1 (MQ=255)
                                cTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACt                                                                                                      <  1:173071/141‑1 (MQ=255)
                                        tCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGa                                                                                              <  2:275119/141‑1 (MQ=255)
                                         cAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGaa                                                                                             <  1:207605/141‑1 (MQ=255)
                                         cAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGaa                                                                                             >  1:253047/1‑141 (MQ=255)
                                            cTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGa                                                                                          <  2:26157/141‑1 (MQ=255)
                                             tAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGAc                                                                                         <  1:971012/141‑1 (MQ=255)
                                              aaTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACt                                                                                        >  2:152706/1‑141 (MQ=255)
                                              aaTTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACt                                                                                        <  1:562194/141‑1 (MQ=255)
                                                 tttATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCa                                                                                     >  1:615081/1‑141 (MQ=255)
                                                   tATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACg                                                                                   >  2:160071/1‑141 (MQ=255)
                                                     ttGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAg                                                                                 <  2:5795/141‑1 (MQ=255)
                                                     ttGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAg                                                                                 >  2:71789/1‑141 (MQ=255)
                                                      tgctgcTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAgg                                                                                <  1:760987/141‑1 (MQ=255)
                                                      tgctgcTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAgg                                                                                >  1:115104/1‑141 (MQ=255)
                                                      tgctgcTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAgg                                                                                <  1:966509/141‑1 (MQ=255)
                                                      tgctgcTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAgg                                                                                >  1:538960/1‑141 (MQ=255)
                                                      tgctgcTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAgg                                                                                >  1:451819/1‑141 (MQ=255)
                                                       gctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGt                                                                               <  2:354114/141‑1 (MQ=255)
                                                        ctgctTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTa                                                                              >  1:721130/1‑141 (MQ=255)
                                                               aaTCGTACCACCAGTAGCTTATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTccc                                                                       <  1:52787/141‑1 (MQ=255)
                                                                           aGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAAc                                                           <  2:118246/141‑1 (MQ=255)
                                                                            gTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACa                                                          >  1:203990/1‑141 (MQ=255)
                                                                              aGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTACCAgg                                                        >  2:361185/1‑141 (MQ=255)
                                                                                 taataaATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGc                                                     <  2:38204/141‑1 (MQ=255)
                                                                                  aataaATCATCTGTAATTAACACACGTTGGCCTGGTTTAATTGCATCTTTGTACATTGTTAACAGATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCa                                                    >  2:154441/1‑141 (MQ=255)
                                                                                   ataaATCATCTGAAATTAACACACGTTGACCGGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCaa                                                   <  1:197517/141‑1 (MQ=255)
                                                                                       atcatcTGTCATTCACACACGTTCACCTGGTTTAATTGCATCTTTCTACATTGTTAAAACCTTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGcc                                               <  1:739018/141‑1 (MQ=255)
                                                                                        tcatcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCa                                              >  1:932881/1‑141 (MQ=255)
                                                                                           tcTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACTTTTGTCCCATACTCTAGGTCCTACTTATAACGAATCATTCCACGAGGTGATTTCCCCTCTTTTCTAACACGTGCACACCCACTc                                           >  1:440280/1‑141 (MQ=255)
                                                                                                 aTTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGTCAATCCCCAtt                                     >  1:48514/1‑141 (MQ=255)
                                                                                                 aTTAACACACGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCAtt                                     >  1:178770/1‑141 (MQ=255)
                                                                                                      cacacGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGTAAAGCCAATCCCCATTGAATa                                >  2:279970/1‑141 (MQ=255)
                                                                                                      cacacGTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATa                                >  1:416371/1‑141 (MQ=255)
                                                                                                         acGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGTTGCAAAGTCAATCCCCATTGAATAAGc                             >  1:768958/1‑141 (MQ=255)
                                                                                                          cGTTGACCTGGTTTAATTGCATCTTTTTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGTCAATCCCAATTGAATAAGCt                            >  2:201322/1‑141 (MQ=255)
                                                                                                           gTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACCTTTGTATTATATTTCGGGTCATACTTATAACGCATGACTTCACCAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTa                           <  1:441411/141‑1 (MQ=255)
                                                                                                           gTTGACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTa                           >  2:400131/1‑141 (MQ=255)
                                                                                                              gACCTGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCAGGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAg                        >  1:265685/1‑141 (MQ=255)
                                                                                                                  tGGTTTAATTGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACa                    >  1:487274/1‑141 (MQ=255)
                                                                                                                          ttGCATCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGa            >  2:165323/1‑141 (MQ=255)
                                                                                                                              aTCTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCAGAACGAATGACGTCACGAGGTAATTTCCCTTCGTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATaaa        <  2:185757/141‑1 (MQ=255)
                                                                                                                                cTTTGTACATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGc      <  1:711903/141‑1 (MQ=255)
                                                                                                                                   tgtaCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCaa   >  1:893458/1‑140 (MQ=255)
                                                                                                                                    gtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGTCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcg  <  2:314128/141‑1 (MQ=255)
                                                                                                                                    gtgCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGTCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCAcg  <  2:53761/141‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                          
AATTATAAATGCAATACCTACTACGATACCGCCTAATTTTTCAACTAATTTTATTGCTGCTTCAATCGTACCACCAGTAGCTAATAAATCATCTGTAATTAACACACGTTGACCTGGTTTAATTGCATCTTTGTGCATTGTTAAAACATTTGTACCATATTCTAGGTCATACTCATAACGAATGACTTCACGAGGTAATTTCCCTTCTTTTCTAACAGGTGCAAAGCCAATCCCCATTGAATAAGCTACAGGACAGCCAATGATAAAGCCACG  >  USA300TCH1516_ALE/1744228‑1744500

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: ‑