BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,514,510	T→A	5.5%	intergenic (+25/‑22)	valU → / → valY	tRNA‑Val/tRNA‑Val

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,514,510	0	T	A	5.5%	963.8 / 4.6	325	intergenic (+25/‑22)	valU/valY	tRNA‑Val/tRNA‑Val
Reads supporting (aligned to +/- strand): ref base T (110/194); new base A (2/19); total (112/213)
Fisher's exact test for biased strand distribution p-value = 1.55e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 332 total aligned reads displayed.

TACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGG  >  CP009273/2514443‑2514575

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTGTCGCCAGCTATATTTGTTGTaaa                                                                >  1:23000987/1‑68 (MQ=18)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTGGCCTGCTAAATTTCTTTTaaa                                                                >  1:27010142/1‑68 (MQ=18)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCTCCAGATAAAATTGTTGTaag                                                                >  1:1214793/1‑67 (MQ=17)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCGTGCTAAATGTCTGGTtaa                                                                >  1:28901298/1‑68 (MQ=17)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCTGCTATATTTGGTGTaaa                                                                >  1:1384535/1‑68 (MQ=17)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCATATATATTTATTGTtaa                                                                >  1:10945411/1‑68 (MQ=17)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTtaa                                                                >  1:20060778/1‑68 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTATTGTaaa                                                                >  1:15847531/1‑68 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCGCGCGAGCTAAATTTCTTGTtaa                                                                >  1:21073977/1‑68 (MQ=18)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTGCTCGCCAGCTAAATTTCTTGTaaa                                                                >  1:9104345/1‑68 (MQ=255)

     ggaggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTGGCGAGCTAAATTTCTTGTaaaaa                                                              >  1:15377762/1‑68 (MQ=255)

       aggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAAt                                                             <  1:5309492/67‑1 (MQ=255)

       aggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAAt                                                             <  1:6880303/67‑1 (MQ=255)

         ggggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAAtgtg                                                          >  1:20630171/1‑68 (MQ=255)

          gggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAAtgt                                                           <  1:18565112/66‑1 (MQ=255)

          gggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAAtgt                                                           <  1:135444/66‑1 (MQ=255)

            gTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTGTTGTAAAAATGTGAAg                                                       >  1:24112153/1‑68 (MQ=255)

             tCGGCGGTTCGATCCCGTCATCACCCACCACTTGCTGGCCTGATATATTTGTTGTAAGAATGTGAAGt                                                      >  1:7971393/1‑68 (MQ=17)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:22968092/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:21918789/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:25571138/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:25168862/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:13253061/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:4845358/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:12852523/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:9386979/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:1047869/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                      <  1:3204217/67‑1 (MQ=255)

                  ggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCg                                                  <  1:5939822/67‑1 (MQ=255)

                  ggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGa                                                 <  1:4399724/68‑1 (MQ=255)

                    ttCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGaa                                                <  1:14382523/67‑1 (MQ=255)

                    ttCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGaa                                                <  1:17695579/67‑1 (MQ=255)

                      cGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTg                                             <  1:3978869/68‑1 (MQ=255)

                      cGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTg                                             <  1:25814024/68‑1 (MQ=255)

                       gATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTgg                                            <  1:5452614/68‑1 (MQ=255)

                          cccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTg                                         >  1:26027945/1‑68 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                        <  1:3285337/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                        <  1:5256367/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                        <  1:17265932/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                        <  1:22312165/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                        <  1:22360901/68‑1 (MQ=255)

                           ccGGCATAACGCCCCAGTTTCTCGCCAGCTAAATTTCTTGTAAAAATGGGAAGTACCGAAGTGTGTGa                                        <  1:1662567/68‑1 (MQ=255)

                               catcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTa                                     >  1:4941825/1‑67 (MQ=255)

                                atcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGc                                   <  1:23839595/68‑1 (MQ=255)

                                 tcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGc                                   >  1:3013510/1‑67 (MQ=255)

                                  cccccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAACTACCGAAGTGGGTGATTAGCTc                                 <  1:1472541/66‑1 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                >  1:18402207/1‑67 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                >  1:14915263/1‑67 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                >  1:19781061/1‑67 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                >  1:16413616/1‑67 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                               <  1:1965770/68‑1 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                               <  1:18202248/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGACGTACCGAAGGGGGTGATTAGCTCAGc                              <  1:13035061/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                              <  1:23506042/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                              <  1:15087678/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                              <  1:17932336/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                              <  1:2778849/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTAAAGAAGTGGGTGATTAGCTCa                                >  1:20802207/1‑66 (MQ=255)

                                     ccaccaATTTCTCCCCATCTAAATTTCTTGTTAAAAGGTGTACACCCGAAGGGGGTGATTAGCTCAGc                              <  1:24950877/68‑1 (MQ=255)

                                     acaccacTTTCTCGAAATCTAAATTTCTTTAAAAACTGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                              <  1:22484063/67‑1 (MQ=255)

                                       accacTTTCTCTCCAGCTAAATTTCTTTTAAAAATGAGACGTACCGAAGTGGGTGATTAGCTCAGCTg                            <  1:885676/68‑1 (MQ=255)

                                        ccacTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTgg                           >  1:6243258/1‑68 (MQ=255)

                                         cacTTTCTCGCCATCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTggg                          <  1:7725855/68‑1 (MQ=255)

                                          acTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                         >  1:41193/1‑68 (MQ=255)

                                          acTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                         >  1:11628517/1‑68 (MQ=255)

                                          acTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                         >  1:9811410/1‑68 (MQ=255)

                                          acTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                         >  1:7093243/1‑68 (MQ=255)

                                           cTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGGAGTACCGAAGTGGGTGATTAGCTCAGCTGGgag                        >  1:28479615/1‑68 (MQ=255)

                                           cTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGgag                        >  1:1218664/1‑68 (MQ=255)

                                           cTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGgag                        >  1:25045754/1‑68 (MQ=255)

                                           cTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGgag                        >  1:23882204/1‑68 (MQ=255)

                                            tttCTCGCCAGCTAAATTTCTTGAAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGgaga                       <  1:14678967/68‑1 (MQ=255)

                                              tctcGCCATCTAAATTTCTATAAAAACCGTGAAGTACCGCAGTGGGTGATTAGCTCAGCTGGGAGAGc                     <  1:25400775/68‑1 (MQ=21)

                                               ctcGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                     >  1:2995405/1‑67 (MQ=255)

                                               ctcGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                     >  1:16277466/1‑67 (MQ=255)

                                               ctcGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGATCAGCTGGGAGAGc                     >  1:8660895/1‑67 (MQ=255)

                                                 cGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCa                    >  1:10132914/1‑66 (MQ=255)

                                                  gCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCAcc                  >  1:136231/1‑67 (MQ=255)

                                                  gCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCAcc                  >  1:19263799/1‑67 (MQ=255)

                                                  gCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCt                 <  1:10017896/68‑1 (MQ=255)

                                                    gaGCTAAATTTCATGTAAAAATGAGTAGTACCCACGGGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:26705413/67‑1 (MQ=18)

                                                    catcTAAATTTCTTTTAAAAATGTGAACTACCGTAGGGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:6645302/65‑1 (MQ=21)

                                                    cAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:11136559/68‑1 (MQ=255)

                                                    cAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:16998726/68‑1 (MQ=255)

                                                    cAGCTAAATTTCTTGTAAAAAAGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:26907378/68‑1 (MQ=255)

                                                    cAGCTAAATTTCTGGTAAAAATGTGAACTACCGAAGGGGGTGATTAGCTCAGCTGGGAGAGCACCTc                <  1:23443189/67‑1 (MQ=25)

                                                    cAGCTAAATATCTTTTAAAACTGTGAACACCCCCAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:3468975/68‑1 (MQ=17)

                                                    cAGCTAAATATCTTTTAAAAATGTGAAGTACCGCAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:11867360/68‑1 (MQ=25)

                                                    cAGATAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:19453883/68‑1 (MQ=255)

                                                    cAGATAAATTTCTTGAAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:24541105/68‑1 (MQ=255)

                                                    aaGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:22346109/67‑1 (MQ=255)

                                                      tatAAATCTCTTGAAAAACAGTGACGTAACGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt             <  1:24471450/66‑1 (MQ=18)

                                                        tAACTTTCCTGTAAAAACGTGAAGTACCGCAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTccc              <  1:8393713/65‑1 (MQ=21)

                                                        tAAATTTCTTGTTAAAATGTGTCGTACCGAAGGGGGTGATTAGGTCAGCTGGGAGAGCACCTCCCTTa           <  1:27603964/68‑1 (MQ=18)

                                                        tAAATTTCTTGTAAAAATGTGAAGAACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTccc              <  1:7441839/65‑1 (MQ=255)

                                                        tAAATTTCATGAAAAAATGTGAAGTACCGAAGGGGGTGATTAGCTCAGCTGGGAGAGCACCTcc               <  1:26582545/64‑1 (MQ=21)

                                                             ttCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagg      >  1:16110094/1‑68 (MQ=255)

                                                             ttCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagg      >  1:11334898/1‑68 (MQ=255)

                                                             ttCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagg      >  1:5760567/1‑68 (MQ=255)

                                                              tCTAGTAAAAAGGTGAAGTACCGACGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagga     <  1:21286636/68‑1 (MQ=18)

TACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGG  >  CP009273/2514443‑2514575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`