BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,386	C→A	6.9%	intergenic (+22/‑14)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,382,386	0	C	A	6.9%	996.7 / 4.6	355	intergenic (+22/‑14)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base C (102/216); new base A (26/8); total (131/224)
Fisher's exact test for biased strand distribution p-value = 7.17e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 379 total aligned reads displayed.

CTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGA  >  CP009273/4382319‑4382451

cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:8036824/68‑1 (MQ=255)

cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:43887236/68‑1 (MQ=255)

cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                                   <  1:22334978/68‑1 (MQ=255)

   gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                                                >  1:12093471/1‑68 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGGTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:15058946/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTTCTGTAAGGCACAg                                                               >  1:26512062/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGTCCCAg                                                               >  1:43291505/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:5989758/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:16386748/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:4465991/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:2113322/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                               >  1:51278103/1‑67 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:40804924/68‑1 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:23323842/68‑1 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:12629934/68‑1 (MQ=255)

     cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTACCGCTACAAAAATTCAAACAGCTGTAAGGCACAg                                                               >  1:20260975/1‑67 (MQ=17)

     cAAGGGCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                              <  1:20640768/68‑1 (MQ=255)

       aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                                            <  1:5517525/68‑1 (MQ=255)

       aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCGCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                                            <  1:26656607/68‑1 (MQ=255)

       aGGTCGGGGTCGCGAGTTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                                            <  1:34890110/68‑1 (MQ=255)

         gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATTTAATGCACAGacca                                                           >  1:38331040/1‑67 (MQ=14)

         gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAACGTGATCTAAGGCACAGagcg                                                           >  1:35157926/1‑64 (MQ=14)

         gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAATTGCTGTAAGGCACACacca                                                           >  1:2204930/1‑67 (MQ=255)

         gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccc                                                           >  1:1394852/1‑66 (MQ=255)

         gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAATGCACACacca                                                           >  1:37740505/1‑67 (MQ=14)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTTATGTAAGACACAcaccac                                                          >  1:46961446/1‑67 (MQ=14)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:14807290/67‑1 (MQ=255)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:32053404/67‑1 (MQ=255)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:24977114/67‑1 (MQ=255)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          >  1:87137/1‑67 (MQ=255)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:5617971/67‑1 (MQ=255)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:37176209/67‑1 (MQ=255)

          tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                          <  1:18588314/67‑1 (MQ=255)

           cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCAccc                                                        <  1:9976816/68‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:41820021/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:46675995/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:36954791/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:47222582/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:9385370/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:34061753/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:32850239/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:34200892/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:11462693/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:27652672/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:1929791/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:22522295/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:19596728/67‑1 (MQ=255)

               gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:20938681/67‑1 (MQ=255)

               gTCGCGAGTGCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:6250377/67‑1 (MQ=255)

               gTCGCGAGTCCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                     <  1:49969824/67‑1 (MQ=255)

                  gcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                                 <  1:49099453/68‑1 (MQ=255)

                    taGTTCGAGTCTCTTTTCCCGCTCCAAAATTTGAAAGTGCTGTAACGCACAGACCACCCAAGCGGGa                                                <  1:33652420/66‑1 (MQ=14)

                    gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                                <  1:29963881/67‑1 (MQ=255)

                    gAGTTCGAGGCTCTTTTCCCGCTCCAAAATTTGAAAGTGCTGTAACGCACAGACCACCCAAGCGGGa                                                <  1:34676680/67‑1 (MQ=14)

                        tCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                                           <  1:8176508/68‑1 (MQ=255)

                        tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTTATGTAAGGACCACACCGCCCAGGGGGGTATAGc                                           >  1:41457708/1‑68 (MQ=9)

                        tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGTCACAGACCACCCAAGCGGGAATAg                                            <  1:22825298/67‑1 (MQ=255)

                        tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                                           <  1:7331721/68‑1 (MQ=255)

                        tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGACCTGTAAGCACCAGACCAACCAACAGGGAATAGc                                           >  1:21782449/1‑68 (MQ=17)

                            gTCTCGTTTCCCCGTCCAAAATTTCAAAGTGCTCTAAGTCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:3573400/68‑1 (MQ=17)

                            gTCGCGTTTCCCGCTCCAAAATTTCAAAGTGCTGTAACGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:4203834/68‑1 (MQ=14)

                            gTCCCGTTTCCCGCCCCAAAATTTTAAAGTGCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAg                                       <  1:2572030/68‑1 (MQ=17)

                             tctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGt                                      >  1:50582937/1‑68 (MQ=255)

                              ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:42965226/66‑1 (MQ=255)

                              ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAg                                       <  1:24351149/66‑1 (MQ=255)

                              ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCCAGCGGGAATAGCTCAGtt                                     >  1:2387044/1‑68 (MQ=255)

                              ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:28532517/66‑1 (MQ=255)

                              ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:33790402/66‑1 (MQ=255)

                              ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                       <  1:1372469/66‑1 (MQ=255)

                              ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                                     <  1:38977505/68‑1 (MQ=255)

                              ctcGTTACCCGCCACAAAATTTTAAATTTCTTTAACTCACATACCACCCAAGCGGGAATAGCTCAg                                       <  1:17932328/66‑1 (MQ=9)

                                cGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                                   >  1:48003895/1‑68 (MQ=255)

                                cGTTTCCCGCTCCAAAATTTGAAAGTCCTGAAACGCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                                   <  1:21357238/68‑1 (MQ=14)

                                 gTTTCGCGCGCCAAATTTTTAAATTGCTGAAAGGAACATACCTCCCAAGCGGGAATAGCTCAGTTGGt                                  <  1:39361971/68‑1 (MQ=9)

                                 gTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                                  <  1:4616424/68‑1 (MQ=255)

                                 gTTTCCCGCCCGAAAATTGTAAAGTGCTTAATGTAACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                                  <  1:48752174/68‑1 (MQ=9)

                                  tttCCCGCTCCAAATTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGAGGGAATAGCTCAGTTGGTa                                 >  1:31520769/1‑68 (MQ=255)

                                  tttCCCGCTCCAAAATTTGAAAGTGCTGTAATGAACAGACCACCCAAGAGGGAATAGCTAAGTTGTTa                                 >  1:44257644/1‑68 (MQ=14)

                                  tttCCCGCTCCAAAATTTGAAAGTGATGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTa                                 >  1:29114611/1‑68 (MQ=255)

                                  tttCCCGCTCCAAAATATTAAAGAGCTGTAATGCACAGACCGCCCAAACGGGAATAGCTCAGTTGTTa                                 >  1:45175105/1‑68 (MQ=14)

                                    tCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                               <  1:15801364/68‑1 (MQ=255)

                                     cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                               >  1:36283553/1‑67 (MQ=255)

                                           ccAAAATTTTAAAGTTCTGTACCTCACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:3058143/68‑1 (MQ=14)

                                           ccAAAATTTTAAAGTGCTGAATGTCACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:23040195/68‑1 (MQ=14)

                                           ccAAAATTTGAAAGTGCTGAAAGCCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                        <  1:27350397/68‑1 (MQ=255)

                                                     aaaGTGCTGTATGGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAgg              <  1:17219970/68‑1 (MQ=255)

                                                     aaaGTGCTGTAAGGCACAGAACACCCAAGCGGGAATAGCTCAGTTGGTAGAGAACGACCTTGCCAAgg              <  1:35880050/68‑1 (MQ=14)

                                                      aaGTTCTGTAACTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGt             <  1:43621342/68‑1 (MQ=11)

                                                      aaGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAgg              <  1:10465889/67‑1 (MQ=40)

                                                      aaGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAgg              <  1:8392024/67‑1 (MQ=40)

                                                       aGTGCTGTAAGGCACAGCCCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTc            >  1:29788704/1‑68 (MQ=255)

                                                          gCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCgt          <  1:47618572/67‑2 (MQ=255)

                                                          gCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCggg         >  1:10081660/1‑68 (MQ=40)

                                                           cTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCgggg        >  1:10587746/1‑68 (MQ=40)

                                                               aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:32598108/1‑68 (MQ=35)

                                                               aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTcgc    >  1:39692446/1‑68 (MQ=35)

                                                               aaGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGCTCGGGGTcgc    >  1:31180346/1‑68 (MQ=25)

                                                                 ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:45724890/1‑68 (MQ=31)

                                                                 ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:6832774/1‑68 (MQ=31)

                                                                 ggCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGa  >  1:44915793/1‑68 (MQ=31)

CTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTCGCGA  >  CP009273/4382319‑4382451

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: `‑`