Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 478,502 C→A 100% D342E (GAC→GAA)  nuoL → NADH‑quinone oxidoreductase subunit L

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE478,5020CA100.0% 170.5 / NA 55D342E (GAC→GAA) nuoLNADH‑quinone oxidoreductase subunit L
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (24/31);  total (24/31)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTAT  >  USA300TCH1516_ALE/478368‑478629
                                                                                                                                      |                                                                                                                               
cAATGTGCATAGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTAt                                                                                                                           >  2:272052/1‑141 (MQ=255)
  aTGTGCATAGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTCTgg                                                                                                                         >  2:685834/1‑141 (MQ=255)
      gCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTgg                                                                                                                     >  1:595767/1‑141 (MQ=255)
      gCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCAAGGTATGGTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTGAATATTCCAAAACAAGCATCTGCGAAAGAAGCTTATGGCTgg                                                                                                                     >  1:305379/1‑141 (MQ=255)
       cATTGTGTTTATATTCAGCAGTGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGa                                                                                                                    <  2:533386/141‑1 (MQ=255)
       cATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTTTTTCTTTTTTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCGGCTAAAGAAACTTATGGCTggg                                                                                                                    >  2:225196/1‑140 (MQ=255)
       cATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGa                                                                                                                    <  1:660068/141‑1 (MQ=255)
            ggTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTc                                                                                                               >  1:113846/1‑141 (MQ=255)
             gtgtATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCa                                                                                                              <  1:377327/141‑1 (MQ=255)
                            cGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAg                                                                                               >  1:145959/1‑141 (MQ=255)
                            cGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAAGCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGTTTATGGCTGGGTTGTCATGGGACGTGTATTAg                                                                                               >  1:465959/1‑141 (MQ=255)
                             gATTATTCATTCAAGATTGCACGGTTTTTTTAAAGCAACATTAGTTTTACAATCAGGTTCTATCGTGAAGCGATTCAAGATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGTATTGTCATGGGACGTGTATTAGc                                                                                              <  1:178338/141‑1 (MQ=255)
                               ttattCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCta                                                                                            <  1:99611/141‑1 (MQ=255)
                               tcattCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCta                                                                                            <  1:285874/139‑1 (MQ=255)
                                  ttCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCtatta                                                                                         >  2:376678/1‑141 (MQ=255)
                                    cATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATc                                                                                       <  1:415104/141‑1 (MQ=255)
                                    cATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATc                                                                                       <  2:670227/141‑1 (MQ=255)
                                    cATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAACCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATc                                                                                       <  2:332959/141‑1 (MQ=255)
                                     aTTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCg                                                                                      >  1:146558/1‑141 (MQ=255)
                                      tttAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGt                                                                                     >  1:568020/1‑141 (MQ=255)
                                       ttAATATTGCACGGTTTTTTTAAAGCAACCTTATTTTTAAAACGAAGTTCTAGGGTAGCGCGATTCTAGATTCGAAAGCAAGGATCTGCTTAATGATCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTg                                                                                    <  2:508226/141‑1 (MQ=255)
                                            atTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCAtt                                                                               >  1:247084/1‑141 (MQ=255)
                                             ttGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTCTCGTGCAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCAttt                                                                              <  2:120788/141‑1 (MQ=255)
                                             ttGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCAttt                                                                              <  2:585271/141‑1 (MQ=255)
                                              tGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTc                                                                             >  1:602570/1‑141 (MQ=255)
                                              tGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCAGTTc                                                                             >  1:318826/1‑141 (MQ=255)
                                                  cGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTAtt                                                                         <  2:344097/141‑1 (MQ=255)
                                                  cGGTATTTTTAAAGAAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTAtt                                                                         >  1:379461/1‑141 (MQ=255)
                                                        ttttAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGAt                                                                   <  2:252396/141‑1 (MQ=255)
                                                         ttcaaaGCAACATTATTTTTACAATCAGGTTCTACCGTAAAGCGAATCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGACCGTCATGGAACGCGTATTAGCTATTATCGTGGCATTCCAATTCTGGagg                                                                  >  2:621697/4‑139 (MQ=255)
                                                          ttAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTTGATgg                                                                 >  2:27568/1‑140 (MQ=255)
                                                          ttAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGa                                                                 >  1:263588/1‑141 (MQ=255)
                                                               gCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGagtagt                                                            <  2:262559/141‑1 (MQ=255)
                                                                cAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTg                                                           <  2:433484/141‑1 (MQ=255)
                                                                     ttattTTTACAATCAGGTTCTATCGGGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGa                                                      <  2:359681/141‑1 (MQ=255)
                                                                         ttttACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTg                                                  <  1:587684/141‑1 (MQ=255)
                                                                            tACAATCAGGTTCTATCGTGAAGCGAGTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCATGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCat                                               <  2:65343/141‑1 (MQ=255)
                                                                                     gTTCTATCGTGAAGCGAATCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGCTTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAgtgt                                      >  1:167882/1‑141 (MQ=255)
                                                                                       tCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTa                                    <  1:665939/141‑1 (MQ=255)
                                                                                           tCGTGAAGCGGTTCAATATTCCAAAACAAGCGGCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTg                                <  2:673203/141‑1 (MQ=255)
                                                                                           tCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTg                                <  2:379461/141‑1 (MQ=255)
                                                                                           tCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTg                                <  2:46035/141‑1 (MQ=255)
                                                                                             gTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGGTTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCa                              <  1:506101/141‑1 (MQ=255)
                                                                                              tGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCAc                             >  1:289869/1‑141 (MQ=255)
                                                                                                      ttCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTa                     >  2:532289/1‑141 (MQ=255)
                                                                                                      ttCAATATTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTa                     <  1:201411/141‑1 (MQ=255)
                                                                                                          atatTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGATTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGAt                 >  1:175238/1‑141 (MQ=255)
                                                                                                            gttCCAAAACAAGCACCTGCTAAACAAGCTGATGTCGTGTTTGTCATGGTACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGATTAGTGACATAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATgg               <  2:230466/140‑1 (MQ=255)
                                                                                                            atTCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATgg               <  1:115339/141‑1 (MQ=255)
                                                                                                             ttCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGt              <  2:247084/141‑1 (MQ=255)
                                                                                                             ttCCAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAACTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGt              >  2:190017/1‑141 (MQ=255)
                                                                                                             taccAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGt              <  1:450024/139‑1 (MQ=255)
                                                                                                                cAAAACAAGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCAt           <  1:512153/141‑1 (MQ=255)
                                                                                                                      aaGCATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTg     <  2:263588/141‑1 (MQ=255)
                                                                                                                         cATCTGCTAAAGAAGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGAAGTGACAGAAGTGCATATGAGGTGGTAAGTGCACTCATTCTAGGATGGTGATTACTTGtgt  >  1:227830/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                               
CAATGTGCATTGGGTGTATATTCAGCAGCGATTATTCATTTAATATTGCACGGTATTTTTAAAGCAACATTATTTTTACAATCAGGTTCTATCGTGAAGCGATTCAATATTCCAAAACAAGCATCTGCTAAAGACGCTTATGGCTGGATTGTCATGGGACGTGTATTAGCTATTATCGTGGCATTTCTATTTTGGATGAGTAGTGACAGAAGTGCATATGAAGTGTTAAGTGCACTCATTCTAGGATGGTCATTACTTGTAT  >  USA300TCH1516_ALE/478368‑478629

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: ‑