BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,384	G→T	6.4%	intergenic (+20/‑16)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,382,384	0	G	T	6.4%	569.9 / 2.3	221	intergenic (+20/‑16)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (63/129); new base T (14/3); total (79/142)
Fisher's exact test for biased strand distribution p-value = 8.70e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 274 total aligned reads displayed.

ACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGA  >  CP009273/4382317‑4382451

aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTTCTGTAAg                                                                     >  1:31770287/1‑68 (MQ=255)

aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                                     >  1:6641825/1‑68 (MQ=255)

aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                                     >  1:4356236/1‑68 (MQ=255)

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

 ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGAGATGTAAgg                                                                    >  1:32217983/1‑68 (MQ=14)

 ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:16069653/68‑1 (MQ=255)

 ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:11171141/68‑1 (MQ=255)

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

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

 ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                    <  1:32099500/68‑1 (MQ=255)

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

  cTTTCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:9270916/68‑1 (MQ=255)

  cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:33125737/68‑1 (MQ=255)

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

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

     gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                                                <  1:276852/68‑1 (MQ=255)

     gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                                                <  1:15243491/68‑1 (MQ=255)

     gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                                                <  1:1627592/68‑1 (MQ=255)

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

       cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAATTGATGTAATGCCCAg                                                               >  1:11260550/1‑67 (MQ=11)

       cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:30204050/1‑67 (MQ=255)

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

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

       cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               <  1:26979434/67‑1 (MQ=255)

       cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:12249025/1‑67 (MQ=255)

       cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:10361015/68‑1 (MQ=255)

       cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:5556045/68‑1 (MQ=255)

       cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:5077922/68‑1 (MQ=255)

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

         aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                                            <  1:8806589/68‑1 (MQ=255)

          ggTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGGACAGacc                                                            >  1:27978065/1‑67 (MQ=255)

           gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              >  1:5777947/1‑64 (MQ=255)

            tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:23548787/67‑1 (MQ=255)

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

                 gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATTAAATGAACACACCACCCAAga                                                    >  1:208504/1‑67 (MQ=14)

                 gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:13231506/67‑1 (MQ=255)

                 gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:31201908/67‑1 (MQ=255)

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

                 gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:25974104/67‑1 (MQ=255)

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

                 gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGAGATATAATGCACAGACCCCCCatgg                                                    >  1:5474433/1‑65 (MQ=14)

                  tCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTTTAATGAACACACCCCCCCAGCg                                                   >  1:34869521/1‑68 (MQ=14)

                    gcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                                 <  1:15571787/68‑1 (MQ=255)

                      gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                                <  1:28702947/67‑1 (MQ=255)

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

                      gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                                <  1:14062290/67‑1 (MQ=255)

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

                       aGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTTCTGTAATGCACAGACCCCCCACGGGGGAAt                                              >  1:19003449/1‑68 (MQ=14)

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

                          tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAATTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                             <  1:29194167/66‑1 (MQ=255)

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

                          tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                             <  1:13515396/66‑1 (MQ=255)

                          tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                             <  1:13082912/66‑1 (MQ=255)

                          tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAg                                            <  1:10596366/67‑1 (MQ=255)

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

                              ggctcGTTTCCCGCTCAAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCa                                        <  1:34570819/65‑1 (MQ=17)

                              gTCTCGTTTCCCGCTCCAAAATTTGATAGTGCTGTAATGAACAGACCACCCAAGCGGGAATATCTCAg                                       >  1:393701/1‑68 (MQ=14)

                                ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:15649546/66‑1 (MQ=255)

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

                                ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:32845612/66‑1 (MQ=255)

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

                                ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:8265858/66‑1 (MQ=255)

                                ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                                     <  1:12477339/68‑1 (MQ=255)

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

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

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

                                ctcGTTTCCCGCTCCAAAATTTGAAAGTGATGTAAGGCACAGACCACCCAAGAGGGAATAGCTCAGtt                                     >  1:1157730/1‑68 (MQ=17)

                                cccGTTTCCCGCTCCAAAATTTTAAAGTGCTGAAAGGCACAGACCACCCAAGCGGGAATAGCTCAGt                                      <  1:8346877/65‑1 (MQ=14)

                                atggTTTCCCGGTCCAAAATTTTAAAGTGCTGAACGCAACATACCACCCACGCGGGAATAGCTCAg                                       <  1:10749784/63‑1 (MQ=9)

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

                                     ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGTTag                                >  1:21984151/1‑68 (MQ=255)

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

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

                                       cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                               >  1:4791088/1‑67 (MQ=255)

                                       cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                               >  1:17517892/1‑67 (MQ=255)

                                            accAAAATTTGAAAGTGCTGAAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa                         <  1:2650660/67‑1 (MQ=255)

                                             acAAAATTTGAAAGTGCTCTAAGCAACAGACCACCCACGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:11934038/67‑1 (MQ=17)

                                              aaaaaTTTTAAAGTGATGTAACGCAGAGACGCACAACGCTTTAATAGCCACGTTGGTAGAGCACGAc                        <  1:7068462/66‑1 (MQ=255)

                                                 aaTTTGAAAGTGCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                    <  1:30126757/68‑1 (MQ=255)

                                                 aaTTTGAAAGTGCTGTAAGGCACAGACCACCCACGCGTGAATAGCTCAGTTGGTAGAGCACGACCTTg                    <  1:5799753/68‑1 (MQ=255)

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

                                                 aaTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCtt                     >  1:14321278/1‑67 (MQ=255)

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

                                                  aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                    >  1:23727215/1‑67 (MQ=255)

                                                       aaaGTGCTGTATGTCACAGACAACCCACGCTGGAATAGCTCAGTTGGTAGAGCACGACCTTGCcaagg              >  1:32583195‑M2/1‑63 (MQ=255)

                                                       aaaGTGCTGTAAGGCACAGCCCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCcaagg              <  1:2024210‑M2/68‑6 (MQ=255)

                                                       aaaGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCcaagg              <  1:30625018‑M2/68‑6 (MQ=255)

                                                       aaaGTGCGGAAACCCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCcaagg              >  1:15007152‑M2/1‑63 (MQ=255)

                                                         aGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCcaaggtc            <  1:23919093‑M2/68‑8 (MQ=255)

                                                           tcctgAAACGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCcaaggtcgt          >  1:16750668‑M2/3‑59 (MQ=255)

                                                            gCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCggg         >  1:31127266/1‑68 (MQ=40)

                                                               gTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTc      <  1:23477413/68‑1 (MQ=39)

                                                                 aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:18452967/1‑68 (MQ=35)

                                                                 aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:6417874/1‑68 (MQ=35)

                                                                 aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:29479233/1‑68 (MQ=35)

                                                                 aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:7036512/1‑68 (MQ=35)

                                                                 aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:26090056/1‑68 (MQ=35)

                                                                   ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:32957125/1‑68 (MQ=31)

                                                                   ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:1966438/1‑68 (MQ=31)

                                                                   ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:14809808/1‑68 (MQ=31)

ACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGA  >  CP009273/4382317‑4382451

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: `‑`