Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 220,447 C→T 7.2% A170T (GCA→ACA)  ipdC ← Indole‑3‑pyruvate decarboxylase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE220,4470CT 7.2% 154.5 / 2.6 56A170T (GCA→ACA) ipdCIndole‑3‑pyruvate decarboxylase
Reads supporting (aligned to +/- strand):  ref base C (27/24);  new base T (2/2);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

GTTAATTTCATGTCCAGTAATGATGATAGGCTGCTTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTTGTGCAACGGTTATATGTGCA  >  USA300TCH1516_ALE/220307‑220571
                                                                                                                                            |                                                                                                                            
gTTAATTTCATGTCCAGTAATGATGATAGGCTGCTTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGc                                                                                                                              <  1:105422/141‑1 (MQ=255)
    atttcatttcCAGTAATGATGTTAGGCTGCTTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACa                                                                                                                          <  2:311102/141‑1 (MQ=255)
         aTGTCCAGTAATGATGATAGGCTGCTTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGAt                                                                                                                     >  1:93279/1‑141 (MQ=255)
          tGTCCAGTAATGATGATAGGCTGCTTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGAtt                                                                                                                    <  1:65404/141‑1 (MQ=255)
                         gtAGGCTGCCTCGCCTGATGCAGTTTAGTGGCTAATACCTCTATATATGTTGAGGCATCCGTATATGTGGTTGCCGTCACTGCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGa                                                                                                     <  1:303865/140‑1 (MQ=255)
                              ctgctTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGCTTGGTAAATGTAACTGAACttg                                                                                                >  2:90894/1‑139 (MQ=255)
                                 ctTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCg                                                                                             >  1:102047/1‑141 (MQ=255)
                                 ctTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCg                                                                                             >  1:374298/1‑141 (MQ=255)
                                 ctTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGCAAATGAACTGGGCg                                                                                             <  1:250181/141‑1 (MQ=255)
                                     gCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCtt                                                                                         <  1:78636/141‑1 (MQ=255)
                                      cTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCttt                                                                                        >  1:224874/1‑141 (MQ=255)
                                         gATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCgg                                                                                     <  1:326384/141‑1 (MQ=255)
                                          aTGCAGTTTCGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCCCTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGCCATCGATTGGTAAATGTAAATGAAATGGGGGTCATTAGGc                                                                                    >  2:148777/1‑141 (MQ=255)
                                           tGCAGTTTAGTTGCTAATAACTCTACATATCTTGATGCATCCGTATATTTAGTAGCCGACACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGAAAATGAACTGGGCGCCTCTCGGCg                                                                                   >  2:64586/1‑141 (MQ=255)
                                                 ttAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCt                                                                             >  2:186059/1‑141 (MQ=255)
                                                  tAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTg                                                                            >  1:129079/1‑141 (MQ=255)
                                                  tAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAAATGGGCGTCTTTCGGCGATTGCTg                                                                            >  1:71779/1‑141 (MQ=255)
                                                              gctctATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAAc                                                                >  1:313014/2‑141 (MQ=255)
                                                              aCTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAGCTGGGCGTCTTTCGGCGATTGCTGTTttaattaatc                                                                >  1:56969/1‑139 (MQ=255)
                                                              aCTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGGAAATGTAAATGAACTGGGCGTCTTTCGGCAATTGCTGTATTAATTAAAc                                                                >  2:65556/1‑141 (MQ=255)
                                                                tctATATATGTTGATGCATCCGTATATTTAGTTGCCGTCATTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTTATTAAACGt                                                              <  1:280411/141‑1 (MQ=255)
                                                                    tatatGTTGATGCATCCGTATATTTAGTTGCCGCCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTa                                                          >  2:337307/1‑141 (MQ=255)
                                                                      tatGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCCTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTAtt                                                        <  2:285246/141‑1 (MQ=255)
                                                                        tGTTGATGCATTCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGTGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTc                                                      >  1:56056/1‑141 (MQ=255)
                                                                        tGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGTGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTc                                                      >  1:217728/1‑141 (MQ=255)
                                                                           tGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGAt                                                                                 <  2:243276/111‑1 (MQ=255)
                                                                           tGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGAt                                                                                 >  1:243276/1‑111 (MQ=255)
                                                                           tGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATGTCGgt                                                   >  1:282896/1‑141 (MQ=255)
                                                                               gCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGgttgtt                                               >  2:277133/1‑141 (MQ=255)
                                                                                cctCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAAGTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTGCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGttgttg                                              <  1:12261/139‑1 (MQ=255)
                                                                                  tCCGTATATTTAGTTGCCGTCACTTCAAGTGGTGACGGAATCTCAATTTCAAAGATTGCGCCATCGATTGGTAAATGTAAATGAACTGAGCGTATTTAGACGATTGCTGTATTAATTAAACAAGGAATTTCGGGTGTAGCa                                            >  2:347864/1‑141 (MQ=255)
                                                                                  tCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCGATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAAATAGGCGTCTTTCGGCGATTGCAGTATTAATTAAACGTGGTATTTCGGCTGTTGCa                                            >  2:209289/1‑141 (MQ=255)
                                                                                  tCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGcc                                            >  2:2696/1‑140 (MQ=255)
                                                                                  tCCGTATATTTAGTTGCCGTCACTTCAAATGGTGACGGTATATCAATTTCAGAGATTGCAGCATCGAATGATAAAGGTAAATGAACTGGGCGTCTTTCGGCTCTTGCCGTATTAATTAAACATGGTATTTCGGTTGTTGCa                                            >  2:187649/1‑141 (MQ=255)
                                                                                   ccGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCAt                                           >  1:81896/1‑141 (MQ=255)
                                                                                   ccGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCAt                                           >  1:135860/1‑141 (MQ=255)
                                                                                     ttataTTTAGTTGCCGTTACTGCAAATGGTCTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCAttt                                         <  2:358113/140‑1 (MQ=255)
                                                                                     gtttatTTACTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCAttt                                         <  2:220063/138‑1 (MQ=255)
                                                                                     gTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCAttt                                         >  1:365168/1‑141 (MQ=255)
                                                                                     gTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCAttt                                         <  2:358144/141‑1 (MQ=255)
                                                                                       atatTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTc                                       <  1:70460/141‑1 (MQ=255)
                                                                                       atatTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTc                                       <  1:176106/141‑1 (MQ=255)
                                                                                                tGCCGTCCCTCTAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGat                              <  2:185395/141‑1 (MQ=255)
                                                                                                tGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGat                              <  1:297035/141‑1 (MQ=255)
                                                                                                     tCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTACTTAAACGTGGTATTTCGGTGGTTGCATTTTCAGGTGTGAtatatc                         >  1:330290/1‑139 (MQ=255)
                                                                                                       aCTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCt                       <  1:219383/141‑1 (MQ=255)
                                                                                                          tCAAATGGTGTCGGTATCTCAATTTCAGAGTTTGCGACATCGATTGGTAAATGTAAATGAACTGGTCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTtgt                    <  2:257540/141‑1 (MQ=255)
                                                                                                          tCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTtgt                    <  2:195640/141‑1 (MQ=255)
                                                                                                          tCAAATGGTGTCGGTATCTCAATTTCAGAGATTGAGACATCGATTGAACCAAGTGGAAGAGCTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTtgt                    <  1:11198/141‑1 (MQ=255)
                                                                                                          tCAAATGGGGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTtgt                    <  1:95619/141‑1 (MQ=255)
                                                                                                           cAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTtgtg                   >  2:334132/1‑141 (MQ=255)
                                                                                                            aaaTGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTTGTGc                  <  1:103580/141‑1 (MQ=255)
                                                                                                              aTGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTTGTGCaa                <  2:81896/141‑1 (MQ=255)
                                                                                                               tGGTGTCGGTATCTCAATTTCAGAGATTGTGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTTGTGCAAc               <  2:56056/141‑1 (MQ=255)
                                                                                                               tGGTGTCGGTATCTCAATTTCAGAGATTGTGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTTGTGCAAc               <  2:217728/141‑1 (MQ=255)
                                                                                                                            tcAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTTGTGCAACGGTTATATGTGCa  >  1:23946/1‑141 (MQ=255)
                                                                                                                            taaaTTGCAGAGATTGCGGCAGCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTTCATTTTCAGGTGTGATATAACCTTGTGCAACGGTTATATGTGCa  <  2:49361/139‑1 (MQ=255)
                                                                                                                                            |                                                                                                                            
GTTAATTTCATGTCCAGTAATGATGATAGGCTGCTTCGCTTGATGCAGTTTAGTTGCTAATAACTCTATATATGTTGATGCATCCGTATATTTAGTTGCCGTCACTTCAAATGGTGTCGGTATCTCAATTTCAGAGATTGCGACATCGATTGGTAAATGTAAATGAACTGGGCGTCTTTCGGCGATTGCTGTATTAATTAAACGTGGTATTTCGGTTGTTGCATTTTCAGGTGTGATATAACCTTGTGCAACGGTTATATGTGCA  >  USA300TCH1516_ALE/220307‑220571

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: ‑