BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	8.1%	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	8.1%	1383.3 / 13.5	497	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (128/310); new base T (23/26); total (151/346)
Fisher's exact test for biased strand distribution p-value = 1.43e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 497 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGCAAg                                                             >  1:4892668/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                             >  1:35013627/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                             >  1:32341629/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATTAAAg                                                             >  1:17674031/1‑68 (MQ=255)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAAATTGAAAg                                                             >  1:14488731/1‑68 (MQ=14)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGt                                                            >  1:32123330/1‑68 (MQ=18)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:29061856/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            >  1:9730344/1‑68 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:5979208/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:10092866/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:22827004/68‑1 (MQ=33)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTTAAAGTGCt                                                         >  1:36601900/1‑68 (MQ=255)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                          <  1:24610794/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                          <  1:21090029/67‑1 (MQ=37)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                         <  1:5124449/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:30085406/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:8248634/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:33108483/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:25285862/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:35850581/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGt                                                       >  1:7607440/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTGTTAAAGTGATGTAA‑g                                                   >  1:4639461/1‑68 (MQ=11)

          ccTTGCCACGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:36367433/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:42108476/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:1600334/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:30972022/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:3145410/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:32835717/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:7044897/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:33921725/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:34237898/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:21675387/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:27701104/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑gg                                                  <  1:38569277/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑g                                                   <  1:9577426/67‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGc                                                 <  1:10814701/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGc                                                 >  1:11472553/1‑68 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGc                                                 <  1:42571741/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGc                                                 <  1:30640147/68‑1 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGcaca                                              <  1:34610548/68‑1 (MQ=255)

                cacggTCGGGGTCGCGAGTTCGAGTCTCGGTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGa                                            <  1:1098981/65‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTTATTTAA‑GGCACAg                                             >  1:25575830/1‑67 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAA‑GGAACAg                                             >  1:26306043/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTa                                                      >  1:14959562/1‑59 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAg                                             <  1:4099060/67‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGa                                            <  1:15197599/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGa                                            <  1:43432072/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGa                                            <  1:27940464/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGAACAg                                             >  1:27203127/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGGGCTGTAA‑GGCCCAg                                             >  1:5622496/1‑67 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGacc                                          <  1:24997346/68‑1 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGacc                                          <  1:13514062/68‑1 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAACGTGCTTTAA‑TGTACAGaccg                                         >  1:24030340/1‑66 (MQ=14)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑TGCCCACacca                                         >  1:16359574/1‑67 (MQ=14)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGaccc                                         >  1:25897949/1‑66 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGaccac                                        <  1:12806958/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGacca                                         <  1:40306550/66‑1 (MQ=255)

                      cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCAccc                                      <  1:28604457/68‑1 (MQ=255)

                      cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCAccc                                      <  1:10287645/68‑1 (MQ=255)

                          ggcgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:37424984/65‑1 (MQ=255)

                          ggcgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:23768169/65‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAACATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:19040165/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑TGGACAGACCACCCAAgg                                  >  1:1959190/1‑67 (MQ=14)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GTAACAGACCACCCACGc                                  >  1:26071867/1‑68 (MQ=17)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:16892265/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:36819863/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:39031995/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:8385064/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:19802210/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:26853366/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAg                                   <  1:11230074/67‑1 (MQ=255)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCg                                 <  1:24180289/67‑1 (MQ=255)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCg                                 <  1:39256583/67‑1 (MQ=255)

                              cgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCggg                               <  1:11916817/67‑1 (MQ=255)

                               tatttCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGa                              <  1:16739781/64‑1 (MQ=255)

                               taGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAA‑GTCACAGACCACCCAAGCGGGa                              <  1:15521719/66‑1 (MQ=17)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATa                           <  1:33690955/66‑1 (MQ=255)

                                       gTCTCGTTTCCCGGGACAAATTTTTAAATTGCTGTAC‑CGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:35649857/68‑1 (MQ=14)

                                       gTCGCGTTTCCCGGTCCAAAATTTTAAAGTTCTGAAA‑GTCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:20301016/68‑1 (MQ=14)

                                       gTCCCGTTACCCGCTCCAAAATTTCAAAGTGCTGTAA‑GGCACATAACACCCAAGCGGGAATAGCTCAg                     <  1:7293678/68‑1 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:20636898/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:22149163/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:37707783/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGATGTAA‑GGAACAGACCACCCAAGAGGGAATATCTCAGtt                   >  1:6204517/1‑68 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAATATGAAAGAAATGTAA‑GACCCACACCACCCAAGGGCGAATAGCTCAGtt                   >  1:4142089/1‑68 (MQ=12)

                                         cccGTTTCGCCCTCCAAAATTTCAAAGTGCTGTAA‑GGCACATACCACCCAAGCGGGAATAGCTCAg                     <  1:13239812/64‑1 (MQ=17)

                                         cccGTTTCCCCCTCCAAAATTTAAAATTTCTGAAC‑CTCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:42970190/64‑1 (MQ=2)

                                          gcGTTTCCCGCTCCAAATTTTTAAAGTGC‑GTAACCTCACAGACCACCCAAGCGGGAATAGCTCAGTTg                  <  1:22628255/67‑1 (MQ=14)

                                            gTTTCCCGCTCCAAAATTTGAAAGTGCTGCAA‑GTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                <  1:1879097/68‑1 (MQ=255)

                                             tttCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                <  1:35501370/67‑1 (MQ=255)

                                               TCCCGGTCCAAAATTTTAAAGTGCTGAAC‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:13987307‑M2/68‑1 (MQ=255)

                                               TCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:16208587‑M2/68‑1 (MQ=255)

                                                CCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             >  1:29594164‑M2/1‑67 (MQ=255)

                                                CCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             >  1:29138445‑M2/1‑67 (MQ=255)

                                                CCCCCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTagag            <  1:18164932‑M2/68‑1 (MQ=255)

                                                  CGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc           >  1:23395325‑M2/1‑67 (MQ=255)

                                                     tCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACg        >  1:7986758/1‑67 (MQ=255)

                                                      ccAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc      <  1:2313230/68‑1 (MQ=255)

                                                          aaTTTTAAAGTTCTGTAA‑GGCACAGACCAACCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg  <  1:902706/68‑1 (MQ=14)

                                                          aaTTTTAAAGTGCTGTAA‑CGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg  <  1:31844808/68‑1 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAA‑GGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  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: `‑`