BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,514,509	G→T	6.5%	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	6.5%	1111.8 / 2.4	367	intergenic (+24/‑23)	valU/valY	tRNA‑Val/tRNA‑Val
Reads supporting (aligned to +/- strand): ref base G (142/189); new base T (5/31); total (147/220)
Fisher's exact test for biased strand distribution p-value = 5.46e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 370 total aligned reads displayed.

TACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGG  >  CP009273/2514443‑2514576

tACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTGCTCGCCATCGA‑AATTTTTTGt                                                                    >  1:5983456/1‑68 (MQ=17)

tACAAGGACGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGt                                                                    <  1:20364049/68‑1 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTGTCGCCAGATATAATTTTTtatag                                                                  >  1:13343292/1‑67 (MQ=14)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCATCTA‑AATTTCGTGTaat                                                                 >  1:17298506/1‑67 (MQ=18)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑TATTTCTTGTaaa                                                                 >  1:15957494/1‑68 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑TATTTCTTGTaaa                                                                 >  1:15036741/1‑68 (MQ=255)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTGCTCGCCAGCTA‑AATTTGGTGTaaa                                                                 >  1:26522724/1‑68 (MQ=18)

   aaGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTACTCGCCTGATA‑AAATTATTGTaaa                                                                 >  1:5534372/1‑68 (MQ=17)

   aaGGAGGGGGTCGGCGGATCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTaaa                                                                 <  1:6902447/68‑1 (MQ=255)

       aggGGGTCGGCTGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAt                                                              <  1:8048517/67‑1 (MQ=255)

       aggGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAt                                                              <  1:23552574/67‑1 (MQ=255)

        gggggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCATCTA‑AATTTCTTGTAAAAAtgt                                                            <  1:4557479/68‑1 (MQ=255)

         ggggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAtgtg                                                           >  1:7900937/1‑68 (MQ=255)

          gggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAtgt                                                            <  1:20749654/66‑1 (MQ=255)

          gggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAtgt                                                            <  1:23072136/66‑1 (MQ=255)

          gggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAtgt                                                            <  1:12112691/66‑1 (MQ=255)

          gggTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAtgt                                                            <  1:25491748/66‑1 (MQ=255)

            gTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGaa                                                         <  1:29337715/67‑1 (MQ=255)

            gTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAg                                                        >  1:8747873/1‑68 (MQ=255)

              gggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:10703737/66‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:18324123/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:17963963/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:4909812/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:3258368/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:12824822/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:29628759/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:11427721/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:2669571/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGt                                                       <  1:9543544/67‑1 (MQ=255)

              cggcggTTCGATCCCGTCATCACCCACCAATTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTTaatt                                                       <  1:7299273/67‑3 (MQ=37)

                  ggTTCGATCCCGTAATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGa                                                  <  1:28529648/68‑1 (MQ=255)

                     tCGATTCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGt                                               >  1:12410538/1‑68 (MQ=255)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCCTTCTA‑AAATTCTTGTAAAAAGGTGAAGTACAGAAGt                                               >  1:8490931/1‑68 (MQ=25)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAg                                                <  1:25999832/67‑1 (MQ=255)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGt                                               <  1:7722730/68‑1 (MQ=255)

                     tCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGt                                               <  1:22271342/68‑1 (MQ=255)

                      cGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTg                                              <  1:14685902/68‑1 (MQ=255)

                         tCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGt                                           <  1:6737481/68‑1 (MQ=255)

                         tCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGt                                           <  1:25087241/68‑1 (MQ=255)

                         tCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGt                                           <  1:1291572/68‑1 (MQ=255)

                         tCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTATTGTAAAAATGTGAAGTACCGAAGTTGGt                                           >  1:16383199/1‑68 (MQ=255)

                          cccGTCATCACCCACCACTTTCTCGCCAGCTA‑TATTTCTTGTAAAAATGTGAAGTACCGAATTGGGtt                                          >  1:8926822/1‑67 (MQ=39)

                          cccGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTggggg                                          >  1:11999992/1‑66 (MQ=255)

                           ccGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGa                                         <  1:27867589/68‑1 (MQ=255)

                             gTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGAtt                                       >  1:25586161/1‑68 (MQ=255)

                               catcaCCCACCACTTTCTCGCGTGCTA‑AATGTCGTGTAAAAATGTGAAGTACCGAAGAGGGTGAtaa                                      >  1:15248053/1‑65 (MQ=255)

                               catcaCCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTa                                      <  1:19411121/67‑1 (MQ=255)

                                atcaCCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGc                                    <  1:23698237/68‑1 (MQ=255)

                                  cacccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTc                                  <  1:1150636/68‑1 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCTAAGTGGGTGATTAGCTCa                                 <  1:19787836/68‑1 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCTAAGTGGGTGATTAGCTCa                                 >  1:27158912/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGTGTGATTAGCTCa                                 >  1:6295535/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                 >  1:28993452/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                 >  1:18549318/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                 >  1:29764363/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                 >  1:14413929/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAAAGTGAAGTACCCAAGTGGGTGATTAGCTCa                                 >  1:508549/1‑68 (MQ=255)

                                   acccaccACTTTCTCGCCAGCTA‑AATTTATTGTGAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                 >  1:21547002/1‑68 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                                <  1:3432785/68‑1 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                                <  1:26225261/68‑1 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                                <  1:10368309/68‑1 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                                <  1:17608397/68‑1 (MQ=255)

                                    cccaccACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                                <  1:18884188/68‑1 (MQ=255)

                                    cccacaACTTTCTCGCCAGCTA‑AATTTCATGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                                <  1:2485290/68‑1 (MQ=255)

                                    cacaccacTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAg                                <  1:19975538/66‑1 (MQ=255)

                                     ccaccaGTTTCTCGGCATCTA‑AATTTCTTTAAAAAATGTCACGTACCGAAGTGGGTGATTAGCTCAGc                               <  1:20572568/68‑1 (MQ=255)

                                     ccaccaCTTTCTGGCGTGATA‑AATTTCTTGAAAAACTTTTAAGTACCCATTTGGGTGATTAGCTCAGc                               <  1:9861674/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCGAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGGGATTAGCTCAGc                               <  1:16882535/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCATCTA‑AATTTCTTGTAATAATGTGAAGTAACGACGTGGGTGATTTGCTCAGc                               <  1:22021096/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTA‑AATTTCTTGTAAATTTGTGAAGTACCGAAGTGGGTGATTAGCTCAGc                               <  1:17820817/68‑1 (MQ=255)

                                     ccaccaCTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCa                                 >  1:22492031/1‑66 (MQ=255)

                                        ccacTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTgg                            >  1:28112480/1‑68 (MQ=255)

                                         cacTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTggg                           >  1:3519142/1‑68 (MQ=255)

                                         cacTTTCTCCCCATCTA‑AATTTCTAGTAAAAATGTGAAGACCCGAAGTGGGTGATTAGCTCAGCTggg                           <  1:28010248/68‑1 (MQ=37)

                                          acTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGga                          >  1:13852242/1‑68 (MQ=255)

                                            tttCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGgaga                        >  1:15365375/1‑68 (MQ=255)

                                             ttCTCCCCATCTA‑AATTTCTTTAAAAAATGTGAAGAACCTCAGTGGGTGATTAGCTCAGCTGGGagag                       <  1:10979847/68‑1 (MQ=21)

                                              tctcGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                      >  1:20268352/1‑68 (MQ=255)

                                              tatcGCCAGCTA‑AATTTCTTGTAAAAATGTGACGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                      <  1:13592689/66‑1 (MQ=255)

                                               ctcGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                      >  1:14211171/1‑67 (MQ=255)

                                               ctcGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGc                      >  1:7755791/1‑67 (MQ=255)

                                                 cGCCAGCTA‑AATTTCTTGAAAAAATGTGAAGTACCGCAGTGGGTGATTAGCTCAGCTGGGAGAGCAcc                   <  1:27545866/68‑1 (MQ=255)

                                                 cGCCAGCGA‑ACTTTCATTTAAAAAAGTCTAGTCCCGCAGTGGGTGATTAGCTCAGCTGGGAGAGCAcc                   <  1:22838864/68‑1 (MQ=12)

                                                  gCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCAcc                   >  1:914709/1‑67 (MQ=255)

                                                  gCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCAcc                   >  1:7173965/1‑67 (MQ=255)

                                                   ccAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTc                 <  1:5674194/68‑1 (MQ=255)

                                                    cAGCTA‑ACTTTCTTGAAAAACAGTGACGTACCGACGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc                <  1:17146415/68‑1 (MQ=18)

                                                    cAGCTA‑AATTTCTTTTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTcc                <  1:27680088/68‑1 (MQ=255)

                                                    cAGCTA‑AATTTCTTGTAAAAATGTCAAGTACCGACGGGGGTGATTAGCTCAGCTGGGAGAGCACCTc                 <  1:10047088/67‑1 (MQ=25)

                                                      tttA‑AATTTCATTTTAATCTGAGACGTACCAAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt              <  1:15456874/66‑1 (MQ=9)

                                                      tttA‑AATTTCAATTAAAAGTGTGAAGTACCGAAGGGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt              <  1:24462150/66‑1 (MQ=18)

                                                        tA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCtt             >  1:1964331/1‑67 (MQ=255)

                                                        tA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCtt             >  1:10164515/1‑67 (MQ=255)

                                                        tA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCt              <  1:11234297/66‑1 (MQ=255)

                                                        tA‑AATTTCATGTAAAAATGTGAAGTACCCAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTccc               <  1:4296008/65‑1 (MQ=255)

                                                         a‑aaTATCTTTTAAAAATGTCAACTACCGCAGGGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTa            <  1:19131577/67‑1 (MQ=17)

                                                           aaTTTCTTTTAAAATTGTGACGTACCCAAGGGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACa          <  1:23866417/68‑1 (MQ=17)

                                                           aaTTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACa          <  1:7045743/68‑1 (MQ=255)

                                                              ttCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagg       <  1:21170214/68‑1 (MQ=255)

                                                              ttCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAagg       >  1:9264294/1‑68 (MQ=255)

TACAAGGAGGGGGTCGGCGGTTCGATCCCGTCATCACCCACCACTTTCTCGCCAGCTA‑AATTTCTTGTAAAAATGTGAAGTACCGAAGTGGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGGGG  >  CP009273/2514443‑2514576

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: `‑`