BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,514,509	G→T	6.3%	intergenic (+24/‑23)	valU → / → valY	tRNA‑Val/tRNA‑Val

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,514,509	0	G	T	6.3%	1164.4 / 4.4	394	intergenic (+24/‑23)	valU/valY	tRNA‑Val/tRNA‑Val
Reads supporting (aligned to +/- strand): ref base G (138/219); new base T (6/31); total (144/250)
Fisher's exact test for biased strand distribution p-value = 6.74e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 396 total aligned reads displayed.

TACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGA  >  CP009273/2514443‑2514572

tACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGt                                                                <  1:26799593/68‑1 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCTCCCACCACTTTCTCGCCCGCTAAATTTGTTGTaaa                                                             >  1:21415153/1‑68 (MQ=18)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTGTCGCGAGATAAAATTGTTGTaaa                                                             >  1:8987128/1‑68 (MQ=17)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTGGCGAGCTAAATTTCTTGTaaa                                                             >  1:24045777/1‑68 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCTCCATATAAAATTTTTGTaaa                                                             >  1:31274820/1‑68 (MQ=17)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTtaa                                                             >  1:20509874/1‑68 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTaaa                                                             >  1:15638577/1‑68 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTaaa                                                             >  1:5969858/1‑68 (MQ=255)

    aggaggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTtaaa                                                            >  1:3644595/1‑68 (MQ=255)

     ggaggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTGTCCTTCTAAAATTCTTGTaaaaa                                                           >  1:32580541/1‑68 (MQ=17)

     ggaggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCATCTAAATTTGGTGTaaaaa                                                           >  1:2232725/1‑68 (MQ=18)

     ggaggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTaaaaa                                                           >  1:3421760/1‑68 (MQ=255)

     ggaggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTACTCGCCAGCTAAATTTATTGTaaaaa                                                           >  1:20324590/1‑68 (MQ=255)

       aggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTGTGGCCATCGAAATGTGTTGTaaaaagg                                                         >  1:12533563/1‑66 (MQ=14)

       aggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTaaaaa                                                           <  1:9408339/66‑1 (MQ=255)

       aggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTaaaaa                                                           <  1:16137575/66‑1 (MQ=255)

         ggggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAAtgtg                                                       >  1:14680841/1‑68 (MQ=255)

          gggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAAtgt                                                        <  1:6661641/66‑1 (MQ=255)

           ggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGa                                                      <  1:18412749/67‑1 (MQ=255)

            gTCGGCGGTTCGATCCCGTCATCACCCGCCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGaa                                                     <  1:14413241/67‑1 (MQ=255)

            gTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGaa                                                     <  1:26153101/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATTACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                   <  1:23365361/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                   <  1:7519791/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                   <  1:12119551/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGt                                                   <  1:33379855/67‑1 (MQ=255)

                  tgTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGa                                              <  1:12001507/67‑1 (MQ=255)

                  ggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCg                                               <  1:25105358/67‑1 (MQ=255)

                    ttCGATCCCGTCATCACCCACCACTTTGTCGCCAGCTATATTTCTTGTTAAAATGTGAAGTAaagaag                                            >  1:25891974/1‑68 (MQ=25)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCGAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGt                                           >  1:7256057/1‑68 (MQ=255)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAg                                            <  1:4604841/67‑1 (MQ=255)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGt                                           <  1:13343765/68‑1 (MQ=255)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGt                                           <  1:4819109/68‑1 (MQ=255)

                      cGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTg                                          <  1:27304206/68‑1 (MQ=255)

                         tCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGt                                       >  1:16930634/1‑68 (MQ=255)

                          cccGTCATCCCCCACCACTTTCGCGCCAGCTAAATTTGTTGTAAAAAGGTGAAGTTCCGAAGTggggg                                      >  1:34609720/1‑66 (MQ=255)

                          cccGTCATCACCCACCACTTACTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTg                                      <  1:2769720/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                     <  1:31607429/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                     <  1:32340521/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                     <  1:10156728/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                     <  1:4080370/68‑1 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                     <  1:12778933/68‑1 (MQ=255)

                            cGTCATCACCCACCACTTTCTGGCCAGCTATATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGGGAt                                    >  1:12265993/1‑68 (MQ=255)

                              tcatcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTa                                  <  1:5272790/68‑1 (MQ=255)

                               catcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTa                                  >  1:8726443/1‑67 (MQ=255)

                               catcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTa                                  >  1:18028460/1‑67 (MQ=255)

                               catcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTa                                  >  1:17454461/1‑67 (MQ=255)

                               catcaCCCACCACTTTCTCGCCAGATAAATTTCTTGTAAAAATGTGAAGTACAGAAGAGGGTTAtaa                                  >  1:19230328/1‑65 (MQ=255)

                               catcaCCCACCACTTACTCGCCAGCTAAAATTGTTGTTAAAATGTGAAGTACAGAAATTGGTGATTa                                  >  1:33203275/1‑67 (MQ=255)

                                atcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGc                                <  1:32723850/68‑1 (MQ=255)

                                atcaCCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGc                                <  1:20009449/68‑1 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCtaa                             >  1:25398785/1‑66 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                             >  1:33060664/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                             >  1:16495569/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                             >  1:24753252/1‑68 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                            <  1:6292485/68‑1 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                            <  1:10381947/68‑1 (MQ=255)

                                    accaccaCTTTCTCGCCAGCTAAATTTCTTTTAAAACTGAGAAGTACCGAAGTGGGTGATTAGCTCAg                            <  1:11785747/67‑1 (MQ=255)

                                    accaccaCTTTATCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                            <  1:33726310/67‑1 (MQ=255)

                                     ccaccaGTTTCTCGCTATCTAACTTTCTTTAAAAATTGTCTCGTCCCGGAGTGGGTGATTAGCTCAGc                           <  1:20919733/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                           <  1:10614118/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGATAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                           <  1:20832392/68‑1 (MQ=255)

                                       accacTTTCTCCCCAGCTAAATTTCTTTTAAAACTGTGACCTACCGAAGTGGGTGATTAGCTCAGCTg                         <  1:1115996/68‑1 (MQ=255)

                                        ccacTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTgg                        >  1:28281881/1‑68 (MQ=255)

                                         gccTTTATCGACATCTAAATTTCATTTAAAAATGTGAACTACCGAAGGGGGTGATTAGCTCAGCTggg                       <  1:17553212/66‑1 (MQ=21)

                                         cacTTTCTCGCCAGCTAAATTTCTTGTAAAACTGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTggg                       <  1:2873028/68‑1 (MQ=255)

                                         cacTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGGGGGTGATTAGCTCAGCTggg                       <  1:30289205/68‑1 (MQ=255)

                                         cacTTTCTCGCCAGCTAAATATCTTGTAAAAATGTGAAGTACCGAAGGGGGTGATTAGCTCAGCTggg                       <  1:23025327/68‑1 (MQ=39)

                                         cacTTTCCCCACAGCTAAATTTCACGTAAAACGGAGAAGTACCGAAGTGGGTGATTAGCTCAGCTggg                       <  1:22145807/68‑1 (MQ=21)

                                          acTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                      >  1:4469955/1‑68 (MQ=255)

                                          acTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                      >  1:18891303/1‑68 (MQ=255)

                                          acTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                      >  1:22761908/1‑68 (MQ=255)

                                            tttCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGgaga                    <  1:9126881/68‑1 (MQ=255)

                                             ttCTGGCCAGCTAAATTTCTCGTTAAATCGTCAACAACCTTCGTGGGTGATTAGCTCAGCTGGGagag                   <  1:31917398/68‑1 (MQ=12)

                                              cctcGCAAGCTAAATTTCATGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                  <  1:13835657/67‑1 (MQ=38)

                                               ctcGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                  >  1:1310592/1‑67 (MQ=255)

                                               ctcGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                  >  1:7740179/1‑67 (MQ=255)

                                               ctcGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                  >  1:28939082/1‑67 (MQ=255)

                                               ctcGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                  >  1:19375224/1‑67 (MQ=255)

                                                  gacAGCTAAATATCATGTAAAACTGAGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCt              <  1:29735646/66‑1 (MQ=25)

                                                  gCCAGCTAACTATCTTGTAAAAATGTGAAGTACCGAAGGGGGTGATTAGCTCAGCTGGGAGAGCACCt              <  1:11006130/68‑1 (MQ=25)

                                                  gCCAGCTAAATTTCTTGTAAAATTGTGTAGTAACGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCt              <  1:28549145/68‑1 (MQ=37)

                                                   ccATCTAAATTTCTTTTTAAATTGTGACGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCt              <  1:33249230/67‑1 (MQ=21)

                                                   acAGCGAAATTTCTAGAAAAAGCCTGAAGTACCGAAGTGGGAGATTAGCTCAGCTGGGAGAGCACCTc             <  1:19679639/67‑1 (MQ=18)

                                                    catcTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc            <  1:28158548/65‑1 (MQ=255)

                                                    catcTAAATATCATGAAAAACTGTGAAGTACCGCAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc            <  1:14959380/65‑1 (MQ=18)

                                                    cAGCTAAATTTCTTGTTAAATTGTGAAGTACCTAAGTGGGTTATTAGCTCCGCTGGGAGAGCACCTc             <  1:3413001/67‑1 (MQ=25)

                                                    cAGCTAAATTTCTTGTAAAAATGTGCAGTACGTAAGTGGGTTATTAGATCAGCTGGGAGAGCACCTc             <  1:5540535/67‑1 (MQ=25)

                                                    cAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc            <  1:7133675/68‑1 (MQ=255)

                                                    cAGCTAAATTTCTTGTAAAAATGAGAAGTCCCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc            <  1:29246711/68‑1 (MQ=255)

                                                    cAGCTAAATTTCTTGTAAAAAAGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc            <  1:26463006/68‑1 (MQ=255)

                                                    cAGCTAAATTTCGTGTAAAACTGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc            <  1:28420106/68‑1 (MQ=255)

                                                    cAGCTAAATATCTTTTAAAACTGAGAAGTCCCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc            <  1:27933292/68‑1 (MQ=21)

                                                      tgtAAATTTCTTGTAAATATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt          <  1:16388892/66‑1 (MQ=255)

                                                      tcTAAATTTCTTTTAAAAATGTGAAGTACCGTAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt          <  1:32902576/67‑1 (MQ=25)

                                                        tAAATTTCTTGTAAAACTGTGAAGTACCTAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTccc           <  1:24542993/65‑1 (MQ=255)

                                                        tAAATTTCTTGTAAAACTGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt          <  1:9259054/66‑1 (MQ=255)

                                                        tAAATTTCTTGTAAAAACGAGAAGACACGACGGGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt          <  1:21635937/66‑1 (MQ=14)

                                                          aaTATCTTTAAAAACTGTGAAGTACCTCAGTGGGTTATTAGCTCAGCTGGGAGAGCACCTCCCTTACa      <  1:15223686/68‑1 (MQ=17)

                                                             ttCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagg   >  1:6481293/1‑68 (MQ=255)

                                                              tCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagga  >  1:29968370/1‑68 (MQ=255)

TACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTAAATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGA  >  CP009273/2514443‑2514572

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: `‑`