BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	10.6%	intergenic (+7/‑29)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,382,371	0	G	T	10.6%	905.0 / 16.8	355	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (94/202); new base T (16/25); total (111/244)
Fisher's exact test for biased strand distribution p-value = 3.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 355 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATT‑TTGAAAg                                                            >  1:715081/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTTAAAg                                                            >  1:33425312/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGCAAg                                                            >  1:32389038/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAg                                                            >  1:27313875/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAg                                                            >  1:7710860/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAg                                                            >  1:12828590/1‑68 (MQ=31)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAg                                                            <  1:32201759/67‑1 (MQ=31)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGt                                                           <  1:5303808/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGt                                                           <  1:19899892/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGt                                                           <  1:8028197/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGt                                                           <  1:25406379/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGGCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGt                                                           <  1:13989586/68‑1 (MQ=18)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATGTTCAAAGt                                                           >  1:9008459/1‑68 (MQ=1)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATT‑TTGAAAGt                                                           >  1:14559183/1‑65 (MQ=18)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGc                                                         <  1:26753519/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGc                                                         <  1:9196314/67‑1 (MQ=37)

    gCAAGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGc                                                         <  1:31524025/67‑1 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGt                                                      <  1:2556926/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGt                                                      <  1:16028776/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGt                                                      <  1:28448118/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGt                                                      <  1:13749834/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGt                                                      <  1:33716739/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGt                                                      <  1:10935763/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGt                                                      >  1:2520314/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGATGt                                                      >  1:829623/1‑68 (MQ=255)

        gACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTaa                                                    <  1:13114665/68‑1 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATT‑TTGAAAGAGATGTAAg                                                   >  1:24006330/1‑68 (MQ=11)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGATGTaat                                                   >  1:19112067/1‑67 (MQ=255)

          ccTTGCCAAGGTCGTGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAgg                                                  <  1:29350995/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTaatg                                                  >  1:4230057/1‑66 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAgg                                                  <  1:30530927/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAgg                                                  <  1:16352347/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAgg                                                  <  1:14938442/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAgg                                                  <  1:11782533/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAgg                                                  <  1:34029515/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGAGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAgg                                                  <  1:14087712/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGATAGTGCTGTAAgg                                                  >  1:7488974/1‑67 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTa                                                     >  1:297074/1‑64 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGc                                                 <  1:24706949/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGc                                                 <  1:10044282/68‑1 (MQ=255)

               ccAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGATGTAATGaacac                                             >  1:34235190/1‑67 (MQ=14)

                cacggTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAg                                             <  1:513747/64‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGATAGTGCTGTAAGGCACAg                                             >  1:18079570/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAg                                             >  1:1760067/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAg                                             >  1:24283145/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGa                                            <  1:5901148/68‑1 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGacc                                          <  1:32685483/68‑1 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGacca                                         >  1:18576404/1‑67 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:9277475/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:33023865/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑ATGAAAGAGCTATAAGGCACACacccc                                        >  1:6048676/1‑65 (MQ=17)

                      cGGGGTAGCGAGCTCGAGACTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGaccacc                                       <  1:3520962/67‑1 (MQ=17)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATT‑TTTAAATTGATGTAAGGCACACACCCCCCAAGc                                  >  1:11920900/1‑68 (MQ=17)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:1546393/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:30885299/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:31646597/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:16886955/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:14456604/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:30142775/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:23385128/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:29213356/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:26243046/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:17323051/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:22816986/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGGCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:31942169/67‑1 (MQ=255)

                             gcgAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                               <  1:8112832/68‑1 (MQ=255)

                               taGTTCGATTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:5512445/66‑1 (MQ=255)

                               gtgTTCGAGTCTCGTTTCCCGATCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:22439407/65‑1 (MQ=255)

                               gAGTTCGAGGCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:23685712/67‑1 (MQ=255)

                                aGTTCCAGGCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAAt                            <  1:23091131/68‑1 (MQ=255)

                                   tCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                           <  1:31274464/66‑1 (MQ=255)

                                   tCGAGTCGCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGAAACGCACAGACCACCCAAGCGGGAATAGc                         <  1:14298461/68‑1 (MQ=14)

                                   gcGAGTCTCGTTTCGCGCTCCAAATT‑TTGAAAGTCCGGTAAGGCACAGACCACCCAAGCGGGAATAGc                         <  1:18722099/67‑1 (MQ=17)

                                     gAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTc                       <  1:2785547/68‑1 (MQ=255)

                                     gAGTCTCGTTACCCGCTCCAAAAT‑TTTAAAGTGCTGAAACTCACAGACCACCCAAGCGGGAATAGCTc                       <  1:17873671/68‑1 (MQ=14)

                                     gAGTCGCGTTTCCCGCTCCAAATT‑TTTAAAGTGCTGAAAGGCACAGACCACCCAAGCGGGAATAGCTc                       <  1:19571060/68‑1 (MQ=14)

                                       gTCTCGTTGACAGGTCCAAAAT‑TTTAAAGTGCTGTAATGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:2117370/68‑1 (MQ=14)

                                         ctcGTTTCCCGCTCCAAAAT‑TTTAAAGTGCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAg                     <  1:3690451/66‑1 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAAT‑TTGAAAGTTCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:25036727/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:9625561/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:22079268/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAAT‑TTCAAAGTGCGGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:12210466/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTACAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:4314791/66‑1 (MQ=255)

                                         atcGTTTCCCCATCAAAAAT‑TTAAAAGTGCTGAAACGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:4573825/65‑1 (MQ=11)

                                           cGTTTCCCGCTCCAAAAT‑TTTAAAGTGCTTTAAGCCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                 <  1:6474595/68‑1 (MQ=17)

                                           cGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                 <  1:9510846/68‑1 (MQ=255)

                                            gTTTCCCGGTAGAAAAT‑TTTAAAGTGCTCAAAGTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                <  1:13619209/68‑1 (MQ=14)

                                            gTTTCCCCCTCGAAATT‑TTTAAAGTGCTGTAACTAACATACCACCCAAGCGGGAATAGCTCAGTTGGt                <  1:29909320/68‑1 (MQ=14)

                                             tttCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCCCACACCACCCAAGCGGGTATAGCGAAGTTGGTa               >  1:22211205/1‑68 (MQ=17)

                                               tCCCGCTCCAAAAT‑TTGAAATTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:8530550/68‑1 (MQ=255)

                                               tCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:27180170/68‑1 (MQ=255)

                                               tCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:15027517/68‑1 (MQ=255)

                                               tCCCGCTCCAAAAT‑TTCAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:21586854/68‑1 (MQ=255)

                                               acccGCGACAAAAT‑TTGAAAGTGCTGTAAGGCACAGAACACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:28252933/67‑1 (MQ=17)

                                                cccGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             >  1:10677410/1‑67 (MQ=255)

                                                  cGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTAAGTTGGTAGAGc           >  1:16119408/1‑67 (MQ=255)

                                                     cagaaaaT‑TTTAAAGTGCTCTAACGCACAGACCAACCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa       <  1:20705608/65‑1 (MQ=14)

                                                      ccAAATT‑TTTAAAGTGCTGTAAGGCACAGACCACCCAATCTGGAATAGCTCAGTTGGTAGAGCACGAc      <  1:2729604/68‑1 (MQ=14)

                                                      ccAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc      <  1:11277787/68‑1 (MQ=255)

                                                           aT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg  >  1:10292988/1‑67 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAT‑TTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

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: `‑`