BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,385	G→T	9.6%	intergenic (+21/‑15)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,382,385	0	G	T	9.6%	614.0 / 2.5	252	intergenic (+21/‑15)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (60/154); new base T (3/27); total (65/187)
Fisher's exact test for biased strand distribution p-value = 4.32e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 293 total aligned reads displayed.

CCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGA  >  CP009273/4382318‑4382451

ccTTGCCATGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:16702318/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:7815427/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:23282449/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:14486779/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:28973738/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:29882276/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:13428066/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:31339256/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:32066938/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:33540887/68‑1 (MQ=255)

ccTTGCCAAGGTCGGGGTCGCGAGGTCGAGTCTCGTGTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:19385994/68‑1 (MQ=255)

acTTGCCCAGGGCGGGGTCGCGAGGTCGACGCCCCGTTCCCGCTCCAAAATTTGACAGTGCTGTAAgg                                                                    <  1:2531699/67‑1 (MQ=12)

 cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:2549435/68‑1 (MQ=255)

 cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:36426182/68‑1 (MQ=255)

 atagCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:30643496/65‑1 (MQ=255)

      cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAATGaacac                                                               >  1:24447001/1‑66 (MQ=14)

      cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGAACAg                                                               >  1:33861284/1‑67 (MQ=255)

      cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:24489485/68‑1 (MQ=255)

      cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:17992025/68‑1 (MQ=255)

      cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:17698881/68‑1 (MQ=255)

      cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGAGCTGTAAGGaacac                                                               >  1:3164432/1‑66 (MQ=14)

      cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTACCCGCTCCAAAATTTGTAAGTGCTGTAAGGCACAg                                                               >  1:26503602/1‑67 (MQ=255)

        aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                                            <  1:34233629/68‑1 (MQ=255)

         ggTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGCAAGTTATGTAAGGGACAGacc                                                            >  1:9145693/1‑67 (MQ=17)

          gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATATAATgaccagacca                                                           >  1:28804158/1‑67 (MQ=14)

           tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:15475896/67‑1 (MQ=255)

           tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          >  1:35800315/1‑67 (MQ=255)

           tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:5644498/67‑1 (MQ=255)

           tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacca                                                           <  1:12754016/66‑1 (MQ=255)

           tCGGGGTCGCGAGTTCGAGTCTCGATTCCCGCTCCAAATTTTGAAATTGATGTAAGAGACAGaccac                                                          >  1:21150346/1‑67 (MQ=14)

                ttCGCGAGTTCGAGTCTCTTTTCCCGCTCCAAAATTTGAAATTCCTGTAAGGCACAGACCACCCAAg                                                     <  1:36688814/66‑1 (MQ=17)

                ggcgcgAGTGCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:4436868/65‑1 (MQ=255)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:28448362/67‑1 (MQ=255)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATTTAAGGCACAGACCCCCCAAga                                                    >  1:5044385/1‑67 (MQ=17)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATTAAATGAACACACCACCCAAGc                                                    >  1:1593417/1‑68 (MQ=14)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:577939/67‑1 (MQ=255)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:39371493/67‑1 (MQ=255)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:38993090/67‑1 (MQ=255)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:32254151/67‑1 (MQ=255)

                gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:35917071/67‑1 (MQ=255)

                  cgcgATTTCGATGCTCGTCTCGGTGTCCATAATTTGATAGAGCTGAAACGCACAGACCACCCAAGCgg                                                  <  1:16151496/68‑1 (MQ=9)

                  cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCgg                                                  <  1:21731520/68‑1 (MQ=255)

                   gcgATTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                                 <  1:27640726/68‑1 (MQ=255)

                   gcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                                 <  1:10100024/68‑1 (MQ=255)

                     taGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                                <  1:14765580/66‑1 (MQ=255)

                     gAGTTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                                <  1:6219732/67‑1 (MQ=255)

                        ttCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                             >  1:27967295/1‑67 (MQ=255)

                         tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAATTTCTGTAATTCACACACCGCCCAAGAGGGAATAGc                                           >  1:29268278/1‑68 (MQ=14)

                         tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                                           <  1:20676044/68‑1 (MQ=255)

                         tCGAGTCTCGTTTCCCGCGCCAAAATTTTAAAGTGCTGTACCTAACATACCACCCAAGCGGGAATa                                             <  1:25970174/66‑1 (MQ=14)

                         gcGAGTCCCGTTTCCCGCTCCAAAATTTCAAAGTGCTGTAACGCACAGCCCACCCAAGCGGGAATAGc                                           <  1:27200634/67‑1 (MQ=14)

                             gTCTCGTTTCCCGCGCCAAATTTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:37316246/68‑1 (MQ=17)

                             gTCTCGTTACCCGCTACAAAATTTAAAAGTGCTGAAACTCACATACCACCCAAGCGGGAATAGCTCAg                                       <  1:10922690/68‑1 (MQ=11)

                             gTCGCGTTTCCCGCTCCAAAATTTGAAATTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:1832668/68‑1 (MQ=255)

                               ctcGTTTCGAGCGCCAAAATTTTAAATTGCTGAAAGTCACATACCACCCAAGCGGGAATAGCTCAg                                       <  1:35084119/66‑1 (MQ=9)

                               ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTTAAACTAAAATACCACCCAAGCGGGAATAGCTCAGt                                      <  1:28026350/67‑1 (MQ=14)

                               ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                                     <  1:3837227/68‑1 (MQ=255)

                               ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:24038831/66‑1 (MQ=255)

                               ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                                     >  1:14869794/1‑68 (MQ=255)

                               ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                                     >  1:34145935/1‑68 (MQ=255)

                               ctcGTTTCCCGCTCCAAAATTTGAAAGAGATTTAATGCACACACCTACCAACCGGGAATAGCGCAGtt                                     >  1:30189827/1‑68 (MQ=9)

                               ctcGTTTCCCGCTCCAAAATTTCAAATTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:7396247/66‑1 (MQ=255)

                               ctcGTTTCCCGCTCCAAAATTTCAAAGTGCTGAAACTCACATACCACCCAAGCGGGAATAGCTCAg                                       <  1:10024946/66‑1 (MQ=14)

                               ctcGTTACCCGCTCCAAAATTTCAAATTGCTGTAAGTCAAAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:15685671/66‑1 (MQ=17)

                               ctcGTATCCCGCTACAAAATTTTAAAGTTCTTTAACTCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:25569873/66‑1 (MQ=14)

                               cgcGTTTCCCGCTCCAAATTTTTAAATTGCTGTATGCCACAGACCAAGCAAGCGGGAATAGCTCAGtt                                     <  1:13570756/66‑1 (MQ=17)

                               cgcGTTACCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:3107656/64‑1 (MQ=255)

                               cccGTTTCCCGCCAGAAAATTTAAAATTTCTGTACCTAACATACGACGAAAGCGGGAATAGCTCAg                                       <  1:3877009/64‑1 (MQ=255)

                               cacGTTACCCCCCCCAAAATTTCAAATTCCTGTAACGCACATACCACCCAAGCGGGAATAGCTCAg                                       <  1:38086793/64‑1 (MQ=9)

                                tcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGCCACAGACCACCCACGCGGGAATAGCTCAGTTg                                    <  1:18815812/68‑1 (MQ=255)

                                tcGTTTCCCGCTCAAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                                     <  1:34646521/67‑1 (MQ=255)

                                 cGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                                   <  1:18605283/68‑1 (MQ=255)

                                  gTTTCCCGCTCCAAAATTTGATAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                                  <  1:5976996/68‑1 (MQ=255)

                                  gTTACCCGCTCCAAATTTTCAAAGTGCTGTACCGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                                  <  1:22419177/68‑1 (MQ=14)

                                     tCCCGCCACAAAATTTGAAATTGCTGTAAGTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                               <  1:16804748/68‑1 (MQ=17)

                                      cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                               >  1:17419100/1‑67 (MQ=255)

                                      cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                               >  1:14629415/1‑67 (MQ=255)

                                       ccGCTCCAAAATTTTAAATTGCTGTAAGTAACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc                             <  1:26411696/68‑1 (MQ=17)

                                           tCCAAAATTTTAAATTTCTGTAAGTAACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa                         <  1:19834985/68‑1 (MQ=17)

                                            ctaaaaTTTCCATGTGCTGTAATGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:8516573/66‑1 (MQ=14)

                                            ccAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:26924736/68‑1 (MQ=255)

                                            ccAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:13117502/68‑1 (MQ=255)

                                            ccAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:13066367/68‑1 (MQ=255)

                                            ccAAAATATCAAAGTGCTGAACGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:11434520/68‑1 (MQ=14)

                                                aaTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                    <  1:2201380/68‑1 (MQ=255)

                                                 aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                    >  1:12879880/1‑67 (MQ=255)

                                                      aaaGTGCGCTAACGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAgg              <  1:13972119/68‑1 (MQ=11)

                                                       aaGTGCGGTAAGGCACATACCACCCACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAgg              <  1:3444501/67‑1 (MQ=14)

                                                        aGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTc            >  1:23373034/1‑68 (MQ=40)

                                                        aGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTc            >  1:19746860/1‑68 (MQ=40)

                                                        aGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTc            >  1:16276200/1‑68 (MQ=40)

                                                             tGTAAGGCACAGACCACCCCAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCgtgc        <  1:6688207/67‑4 (MQ=255)

                                                                aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:4161118/1‑68 (MQ=35)

                                                                aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:6543587/1‑68 (MQ=35)

                                                                aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:39412215/1‑68 (MQ=35)

                                                                aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:2485296/1‑68 (MQ=35)

                                                                aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:10439611/1‑68 (MQ=35)

                                                                  ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:19898486/1‑68 (MQ=31)

                                                                  ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:12100045/1‑68 (MQ=31)

                                                                  ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:29408096/1‑68 (MQ=31)

CCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGA  >  CP009273/4382318‑4382451

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: `‑`