BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	6.5%	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	6.5%	977.6 / 2.9	334	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (100/200); new base T (15/13); total (115/219)
Fisher's exact test for biased strand distribution p-value = 3.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 334 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAg                                                            >  1:22912131/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                            >  1:4012916/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                            >  1:30169364/1‑68 (MQ=31)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGt                                                           >  1:2165712/1‑68 (MQ=18)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:25988560/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:19015980/68‑1 (MQ=33)

 agagCAAGACCTTGCGAAGGTGGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:31482609/68‑1 (MQ=11)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           >  1:32141051/1‑67 (MQ=33)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           >  1:1393389/1‑67 (MQ=33)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                         <  1:16603474/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                         <  1:14270966/67‑1 (MQ=37)

     cACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           >  1:34491080/1‑64 (MQ=33)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCttt                                                      >  1:18515268/1‑66 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:31845772/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:2917226/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      >  1:29064005/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:15533473/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:4609563/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:8540190/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:32786251/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTACAAAATTTGAAAGTGCTGt                                                      <  1:16889964/68‑1 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGCTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:29929105/68‑1 (MQ=255)

         cccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:26827084/64‑1 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTATAAg                                                   >  1:5732616/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATGTAAg                                                   >  1:3623076/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGATAGTGCTGTAAg                                                   >  1:27860709/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                   >  1:15636383/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAAg                                                   >  1:7270532/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGAGATGTAAg                                                   >  1:12437982/1‑68 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTGCAAAATTTGAAAGTGCTGTAAgg                                                  >  1:437784/1‑68 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:12596687/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:27327358/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:31189341/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:16460386/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:7017541/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:12065725/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                   >  1:11895157/1‑67 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                 <  1:1799044/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                 <  1:1986971/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                 <  1:33138833/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAATGCTGTAAGGc                                                 >  1:25096193/1‑68 (MQ=255)

               ccAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGTGATGTAAGGGACAg                                             >  1:14851741/1‑68 (MQ=17)

                cAAGGTCTGGGTCGCGAGTTCTAGTCTCGTTTTCATCTGCAATATTTGTAAGTTGTGTAATGCACAGa                                            <  1:2068245/68‑1 (MQ=9)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTATGAAAGTGCTGTAAGGCACAg                                             >  1:12971944/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTTTAAGGAACAg                                             >  1:294366/1‑67 (MQ=17)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                             <  1:7158865/67‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                             >  1:23183004/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                             >  1:25734273/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:33022465/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:10051017/68‑1 (MQ=255)

                 aaGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            >  1:5525529/1‑67 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                          <  1:5173396/68‑1 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGATTTAAGGAACAGaccg                                         >  1:11050643/1‑66 (MQ=17)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:26277835/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:23487926/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:32932771/67‑1 (MQ=255)

                        gggTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAATGCACAGACCCACCaa                                    >  1:32433544/1‑68 (MQ=14)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:31324819/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:10630720/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:13116632/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:5797237/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:26790167/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:4296191/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:4813571/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:15144600/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:1463373/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGc                                  >  1:28548053/1‑68 (MQ=255)

                               taGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:9415022/66‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:2464279/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:6622190/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:34069837/67‑1 (MQ=255)

                                aGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAATGCACAGACCACCCAAGCGGGAAt                            >  1:18287513/1‑68 (MQ=255)

                                  ttCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:21298305/40‑1 (MQ=255)

                                   tCGAGTCTCGTTTCCCGCTCCAAATTGTGAAATTGATTTAATGAACAGACCACCCAACAGGGAATatg                         >  1:6288065/1‑66 (MQ=9)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                           <  1:8047446/66‑1 (MQ=255)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                         <  1:24237054/68‑1 (MQ=255)

                                     gcgTCTCGTTACCCGCTCCAAATTTTGAAAGTGCTGTAACGCACAGACCACCCACGCGGGAATAGCTc                       <  1:13496942/66‑1 (MQ=14)

                                       gTCTCGTTACCAGCTCCAAAATTTTAAATTCCTGAAACTCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:13585224/68‑1 (MQ=14)

                                       gTCGCGTTTCCCGCGACAAATTTTTAAATTGCGGAAAGTCACATACCACCCAAGCGGGAATAGCTCAg                     <  1:16035718/68‑1 (MQ=9)

                                       gTCCCGTTTCCCGGTACAAAATTTCAAAGTGCTCTACCGCACATACCACCCAAGCGGGAATAGCTCAg                     <  1:11429080/68‑1 (MQ=14)

                                       gTCCCGTTTCCCGCCCCAAAATTTCAAAGTGCTCTAAGGAACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:11227918/68‑1 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:27160887/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:10441901/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:33903923/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:30233896/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                   >  1:18946604/1‑68 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGAAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:31017283/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGATGTAAGGCACAGACCACCCAAGCGGGAAAAGCTCAGtt                   >  1:28112355/1‑68 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAATTTCAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:32371991/66‑1 (MQ=255)

                                            gTTTCCCGCTCCAAAATTTCAAAGTGCTGAAAGTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                <  1:17431525/68‑1 (MQ=14)

                                             tttCCCGCGCCAGAATATGAAAGTGCTGTAATGAACAGAGCCCCCAAGGGGGAATAGCTAAGTTGTTa               >  1:23901198/1‑68 (MQ=255)

                                              ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTag              >  1:27569410/1‑68 (MQ=255)

                                               tCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:3078383/68‑1 (MQ=255)

                                               tCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:8345048/68‑1 (MQ=255)

                                               tCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:903629/68‑1 (MQ=255)

                                               tCCCCCACCAAAATTTTAAAGTGCTTAAACGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:34788592/68‑1 (MQ=14)

                                                      ccAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc      <  1:23672940/68‑1 (MQ=255)

                                                          aaTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCtt   >  1:34395649/1‑67 (MQ=255)

                                                          aaTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg  <  1:22345107/68‑1 (MQ=255)

                                                           aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg  >  1:16270809/1‑67 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  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: `‑`