BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	7.6%	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	7.6%	1531.0 / 15.6	549	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (156/324); new base T (24/28); total (182/367)
Fisher's exact test for biased strand distribution p-value = 6.31e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 549 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGC  >  CP009273/4382308‑4382434

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTTAAAg                                                             >  1:35150550/1‑68 (MQ=255)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAg                                                             >  1:50172399/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAg                                                             >  1:17381520/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                             >  1:38049085/1‑68 (MQ=31)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGATAGt                                                            >  1:31221759/1‑68 (MQ=255)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:10685647/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:19720643/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:26201773/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:43999671/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:15631927/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:5775266/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:47575369/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:1253484/68‑1 (MQ=33)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGt                                                            >  1:30088477/1‑67 (MQ=18)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                           <  1:34282844/66‑1 (MQ=35)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                          <  1:29042050/67‑1 (MQ=37)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                          <  1:33141834/67‑1 (MQ=37)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                         <  1:48239382/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:49443300/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:44403660/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                       <  1:5615086/68‑1 (MQ=40)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                    >  1:18335613/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                    >  1:35988330/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                    >  1:35485102/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                    >  1:45795240/1‑68 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCTAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGGAAgg                                                   <  1:38527321/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:9622074/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:25641885/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:36397464/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:36893230/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:38945391/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:40078023/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:41854660/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:45479669/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:25023499/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                   <  1:22221393/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                    >  1:34636517/1‑67 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:20323891/55‑1 (MQ=33)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                            <  1:27923097/55‑1 (MQ=33)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                               <  1:22753564/68‑1 (MQ=255)

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

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

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                             <  1:22370653/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                             <  1:28320363/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                             <  1:26615541/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATTTAAGGAACAg                                              >  1:21760051/1‑67 (MQ=14)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                           <  1:2698787/68‑1 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                           <  1:33733563/68‑1 (MQ=255)

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

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAATTGATGTAAGGCACAGaccg                                          >  1:37188124/1‑66 (MQ=17)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGTCACAGacca                                          >  1:24541147/1‑67 (MQ=255)

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

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

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

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                         <  1:43750064/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                         <  1:892748/67‑1 (MQ=255)

                      cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCAccc                                       <  1:34112563/68‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCacg                                    <  1:16940919/67‑3 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:17589364/67‑1 (MQ=255)

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

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:41403285/67‑1 (MQ=255)

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

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:8055375/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:10144954/67‑1 (MQ=255)

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

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                    <  1:24124733/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGc                                   >  1:1494710/1‑68 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGAACAGACCACCCATGc                                   >  1:7771279/1‑68 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATATAATGAACAGACCACCCAAGc                                   >  1:5507443/1‑68 (MQ=14)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCgg                                 <  1:21949410/68‑1 (MQ=255)

                             gcgAGATCGAGGCTCGTTTCCAGATCCAAAATTTGAAAGTGCTGTAAGTCACAGACCACCCAAGCggg                                <  1:14400183/68‑1 (MQ=17)

                              cgAGTTCGAGTCTCGTTTCCCTCTCAAAAATAAGAAACTCCTGTAAGGCACAGAAAACCCAGCCGGGa                               >  1:4483183/1‑68 (MQ=12)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                               <  1:16252367/67‑1 (MQ=255)

                                   gcGAGTCTCGTTTCGCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                            <  1:31651570/65‑1 (MQ=17)

                                       gTCTCGTTTCCCGCACCAAATTTTCAAAGTGCGGTAACGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:19451743/68‑1 (MQ=14)

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

                                        tctcGTTTCCCGCTCCAAAATATTAAAGTGCTGAAATGGACAGACCACCCAAGCGGGAATAGCGCAGt                     >  1:20641184/1‑68 (MQ=14)

                                         ctcGTTTCCCGCTCCAAATTTTTAAATTGCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAg                      <  1:6538899/66‑1 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGTCACATACCACCCAAGCGGGAATAGCTCAg                      <  1:47122114/66‑1 (MQ=17)

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

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

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

                                         ctcGTTTCCCGCTCAAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                      <  1:32740840/66‑1 (MQ=255)

                                         ctcGTTACCCGCCCCAAAATTTTAAATTTCTTAAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                    <  1:39394573/68‑1 (MQ=14)

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

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

                                            gTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGAACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                 >  1:7132879/1‑68 (MQ=255)

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

                                              ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTag               >  1:2287061/1‑68 (MQ=255)

                                               acccGCCACAAAATCTGAAAGTTCTGTAAGGCACATACCACGCACGCGGGAATAGCTCAGTTGGTaga              <  1:50669784/67‑1 (MQ=17)

                                                cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga              >  1:29874654/1‑67 (MQ=255)

                                                 ccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc            <  1:2115463/68‑1 (MQ=255)

                                                  cGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc            >  1:43333059/1‑67 (MQ=255)

                                                     tCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa        <  1:2331304/68‑1 (MQ=255)

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

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

                                                      acAAATTTTAAAATTTCTGAAAGGAAAATACCAACCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc       <  1:8267061/67‑1 (MQ=2)

                                                      acAAAATTTTAAATTGCTGAAACGCACATACCAAGCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc       <  1:18926549/67‑1 (MQ=14)

                                                         aaaTTTGAAAGTGCTGTAAGGCACAGACCACCCACGCGGGAATAGCTCAGTTGGTAGAGCACGACCtt    <  1:6107663/68‑1 (MQ=255)

                                                           aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCTGGAATAGCTCAGTTGGTAGAGCACGACCtgg   >  1:48567676/1‑65 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGC  >  CP009273/4382308‑4382434

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: `‑`