BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	639,592	C→G	13.5%	A33G (GCC→GGC)	USA300HOU_RS03045 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	639,592	0	C	G	13.5%	278.5 / 29.5	89	A33G (GCC→GGC)	USA300HOU_RS03045	hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (34/43); new base G (6/6); total (40/49)
Fisher's exact test for biased strand distribution p-value = 7.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAGAGAAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGCTAACCATAA  >  USA300TCH1516_ALE/639502‑639682

aTAGAGAAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGc                                                                                            <  1:4061920/91‑1 (MQ=255)

aTAGAGAAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGc                                                                                            <  1:4062085/91‑1 (MQ=255)

 tAGAGAAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGcc                                                                                           <  1:1175386/91‑1 (MQ=255)

  agagAAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCca                                                                                          <  1:2988081/91‑1 (MQ=255)

   gagaAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCcat                                                                                         <  1:847916/91‑1 (MQ=255)

    agaAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCcata                                                                                        <  1:3238531/91‑1 (MQ=255)

     gaAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCcatac                                                                                       <  1:1713023/91‑1 (MQ=255)

     gaAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCcatac                                                                                       >  1:1388752/1‑91 (MQ=255)

      aaaCTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCcataca                                                                                      <  1:3100955/91‑1 (MQ=255)

      aaaCTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCcataca                                                                                      >  1:1049785/1‑91 (MQ=255)

       aaCTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGGcatacat                                                                                     <  1:680610/91‑1 (MQ=255)

         cTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGGCATACatat                                                                                   <  1:896017/91‑1 (MQ=255)

         cTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGGCATACatat                                                                                   <  1:2838789/91‑1 (MQ=255)

          tttAATAGCACGATTTGAGCAAGAAGTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACatata                                                                                  <  1:1783758/91‑1 (MQ=255)

          tttAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGGCATACatatg                                                                                  <  1:1224681/91‑2 (MQ=255)

          tttAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGGCATACatatg                                                                                  <  1:1224220/91‑2 (MQ=255)

          tttAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGGCATACatatg                                                                                  <  1:1224147/91‑2 (MQ=255)

           ttAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACatatat                                                                                 >  1:2905839/1‑91 (MQ=255)

            tAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATAtt                                                                                <  1:912392/91‑1 (MQ=255)

            tAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATAtt                                                                                <  1:2386353/91‑1 (MQ=255)

             aaTAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGTATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTa                                                                               >  1:1757369/1‑91 (MQ=255)

              aTAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCCTACATATATTaa                                                                              <  1:3208281/91‑1 (MQ=255)

               tAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAAc                                                                             >  1:2124616/1‑91 (MQ=255)

                 gCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACAt                                                                           >  1:407646/1‑91 (MQ=255)

                  cACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACACATATTAACATc                                                                          >  1:3765043/1‑91 (MQ=255)

                    cGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCtt                                                                        <  1:3634885/91‑1 (MQ=255)

                    cGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCtt                                                                        <  1:2918286/91‑1 (MQ=255)

                     gAATTGAGCAAGAATTAGTACAAGCAGGGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCttt                                                                       <  1:1223506/91‑1 (MQ=255)

                     gAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCttt                                                                       >  1:1959942/1‑91 (MQ=255)

                     gAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCttt                                                                       <  1:3042822/91‑1 (MQ=255)

                      aaTTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTta                                                                      <  1:2133387/91‑1 (MQ=255)

                      aaTTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTta                                                                      <  1:2133424/91‑1 (MQ=255)

                       aTTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTtat                                                                     <  1:2054913/91‑1 (MQ=255)

                       aTTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTtat                                                                     <  1:2054188/91‑1 (MQ=255)

                       aTTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTtat                                                                     <  1:2054348/91‑1 (MQ=255)

                            gCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCt                                                                >  1:361039/1‑91 (MQ=255)

                               aGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCa                                                             >  1:3365/1‑91 (MQ=255)

                               aGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCa                                                             >  1:3299/1‑91 (MQ=255)

                                  aTTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACa                                                          <  1:228033/91‑1 (MQ=255)

                                   ttAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACAt                                                         <  1:1102433/91‑1 (MQ=255)

                                   ttAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACAt                                                         <  1:3523349/91‑1 (MQ=255)

                                   ttAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACAt                                                         <  1:4078945/91‑1 (MQ=255)

                                   ttAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACAt                                                         <  1:1710188/91‑1 (MQ=255)

                                   ttAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACAt                                                         <  1:4078978/91‑1 (MQ=255)

                                      gTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCaa                                                      <  1:441182/91‑1 (MQ=255)

                                           agcagagcagGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATaca                                                 <  1:1696170/91‑1 (MQ=255)

                                            gcagagcagGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATacac                                                <  1:906463/91‑1 (MQ=255)

                                               gagcagGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATAcaccac                                             <  1:568637/91‑1 (MQ=255)

                                                agcagGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACcaca                                            >  1:3517352/1‑91 (MQ=255)

                                                agcagGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACcaca                                            >  1:446489/1‑91 (MQ=255)

                                                 gcagGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACat                                           <  1:1984839/91‑1 (MQ=255)

                                                 gcagGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACat                                           <  1:2005437/91‑1 (MQ=255)

                                                   agGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACatat                                         >  1:4080504/1‑91 (MQ=255)

                                                   agGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACatat                                         >  1:1326727/1‑91 (MQ=255)

                                                     gCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTg                                       >  1:3930982/1‑91 (MQ=255)

                                                        caGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTg                                    >  1:4121852/1‑91 (MQ=255)

                                                        caGCATGACCATGACATTGAAAAACATATGTATGCCATACATATATTAACATCTTTATCTGCTTCAACATCAAATACACCACATATTGGTg                                    >  1:3532359/1‑91 (MQ=255)

                                                         aGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGa                                   <  1:3504693/91‑1 (MQ=255)

                                                         aGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGa                                   <  1:2209905/91‑1 (MQ=255)

                                                         aGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGa                                   <  1:3505892/91‑1 (MQ=255)

                                                             tgaccatgacTTTGAAAAACATATGTATGCCATACATATATTAACACCTTTATATGCTTCAACATCAAATACACCACATATTGGTGaacaa                               >  1:3293713/1‑91 (MQ=255)

                                                             tgaccatgacTTTGAAAAACATATGTATGCCATACATATATTAACACCTTTATATGCTTCAACATCAAATACACCACATATTGGTGaacaa                               >  1:3293931/1‑91 (MQ=255)

                                                              gactatgacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATTTTGGTGaacaac                              <  1:3207813/91‑1 (MQ=255)

                                                              gacgatgacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATTTTGGTGaacaac                              <  1:3207856/91‑1 (MQ=255)

                                                               accatgacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAacaaca                             >  1:730496/1‑91 (MQ=255)

                                                                ccatgacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAAcaacaa                            >  1:3817534/1‑91 (MQ=255)

                                                                ccatgacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAAcaacaa                            >  1:3816824/1‑91 (MQ=255)

                                                                 catgacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACaaa                           <  1:3173766/91‑1 (MQ=255)

                                                                  atgacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAAt                          >  1:769217/1‑91 (MQ=255)

                                                                    gacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGa                        >  1:1859459/1‑91 (MQ=255)

                                                                    gacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGa                        <  1:1624165/91‑1 (MQ=255)

                                                                    gacTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGa                        >  1:3845522/1‑91 (MQ=255)

                                                                      cTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAAt                      <  1:2784081/91‑1 (MQ=255)

                                                                        ttGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGACtcg                    >  1:3727376/1‑91 (MQ=255)

                                                                        ttGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAAtcg                    <  1:2444633/91‑1 (MQ=255)

                                                                        ttGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAAtcg                    >  1:382910/1‑91 (MQ=255)

                                                                         tGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAAtcgt                   <  1:1208133/91‑1 (MQ=255)

                                                                           aaaaaCATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAAtcgtcg                 >  1:982499/1‑91 (MQ=255)

                                                                            aaaaCATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATcgtcgt                >  1:3912952/1‑91 (MQ=255)

                                                                             aaaCATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTa               <  1:3261865/91‑1 (MQ=255)

                                                                                tatatGTATGGCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGGGAACAACAAATGAATCGTCGTATTg            >  1:3847417/2‑91 (MQ=255)

                                                                                 atatGTATGGCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:2631298/1‑91 (MQ=255)

                                                                                 atatGTATGGCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:463301/1‑91 (MQ=255)

                                                                                 atatGTATGGCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:463779/1‑91 (MQ=255)

                                                                                 atatGTATGGCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:465695/1‑91 (MQ=255)

                                                                                 atatGTATGGCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:565863/1‑91 (MQ=255)

                                                                                 atatGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:3391138/1‑91 (MQ=255)

                                                                                 atatGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:4033648/1‑91 (MQ=255)

                                                                                 atatGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGc           >  1:1712621/1‑91 (MQ=255)

                                                                                      tatgCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGCTAAcc      <  1:438739/91‑1 (MQ=255)

                                                                                      tatgCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGCTAAcc      <  1:3340422/91‑1 (MQ=255)

                                                                                       atgCCATACTTATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGCTAACCa     >  1:2091742/1‑91 (MQ=255)

                                                                                          ccATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGCTAACCATaa  >  1:3842998/1‑91 (MQ=255)

ATAGAGAAACTTTAATAGCACGAATTGAGCAAGAATTAGTACAAGCAGAGCAGGCACAGCATGACCATGACTTTGAAAAACATATGTATGCCATACATATATTAACATCTTTATATGCTTCAACATCAAATACACCACATATTGGTGAACAACAAATGAATCGTCGTATTGCTAACCATAA  >  USA300TCH1516_ALE/639502‑639682

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`