BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	9.2%	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	9.2%	1501.2 / 18.0	562	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (157/329); new base T (28/34); total (185/377)
Fisher's exact test for biased strand distribution p-value = 4.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 565 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAG  >  CP009273/4382308‑4382438

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAg                                                                 >  1:3637520/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                 >  1:10040031/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                 >  1:23501788/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                 >  1:2887685/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                 >  1:41838671/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                 >  1:917625/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                                 >  1:47707206/1‑68 (MQ=31)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCTAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                                <  1:19217011/68‑1 (MQ=18)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGt                                                                >  1:6654291/1‑68 (MQ=18)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                                <  1:39468244/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                                <  1:3665841/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                                <  1:6236137/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                                >  1:1695412/1‑68 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGGCGCGTGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                                <  1:47027780/68‑1 (MQ=255)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTaaatgt                                                               >  1:3135604/1‑65 (MQ=0)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTg                                                               >  1:25102315/1‑68 (MQ=25)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCATTTCCCGCTCCAAAATTTGAAAGTg                                                               <  1:51203375/66‑1 (MQ=25)

    cctcGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                              <  1:52011619/64‑1 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                             <  1:51681562/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                             <  1:30194422/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                           <  1:11026219/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                           >  1:38401419/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                           <  1:56403049/68‑1 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGGCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                           <  1:57367814/68‑1 (MQ=255)

      aCGACCGTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                           <  1:50239771/68‑1 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTGTAAg                                                        >  1:10853121/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTTTAAg                                                        >  1:21904603/1‑68 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:57018687/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:33466879/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:34906346/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:37237580/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:7332217/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:7687926/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:20933166/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:49930438/68‑1 (MQ=255)

          ccTTGCCAAGGGCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                       <  1:42968447/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                      <  1:54035681/68‑1 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                                   <  1:28394175/68‑1 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                                   <  1:14483457/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTTAAAGTGCTGTAATGAACAg                                                  >  1:3379401/1‑67 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTTCTGTAAGGCACAg                                                  >  1:57963427/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGATGTAAGGCACAg                                                  >  1:17257712/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGAGATGTAATGAACAg                                                  >  1:18462387/1‑67 (MQ=11)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                  >  1:48345598/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                  >  1:44630648/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                 <  1:24552561/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                 <  1:36056370/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                 <  1:11998435/68‑1 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAATTGCTGTAAGGCACAGacca                                              >  1:25541174/1‑67 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacca                                              >  1:53690498/1‑67 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGAACACaccc                                              >  1:5458345/1‑66 (MQ=17)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                             <  1:33896994/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGAACAGaccac                                             >  1:421252/1‑67 (MQ=255)

                     tCGGGCTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGTCACAGaccac                                             <  1:27594286/67‑1 (MQ=255)

                      cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccacc                                            <  1:49045067/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTTAAAGTGCTGTAATAAACACAccaaccaaca                                       >  1:43830877/1‑66 (MQ=14)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                        <  1:24117721/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                        <  1:1628516/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                        <  1:13018442/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                        <  1:31652425/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                        <  1:20771365/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGc                                       >  1:49386277/1‑68 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAAGGAACACACCACCCAAGc                                       >  1:2628546/1‑68 (MQ=17)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGGGCTGTAAGGCACAGACCACCCAAGc                                       >  1:6793246/1‑68 (MQ=255)

                           tCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATTTAAGGAACACACCACCCAAGc                                       >  1:23023863/1‑67 (MQ=17)

                            cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCgg                                     <  1:36955407/68‑1 (MQ=255)

                             gctaGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                    <  1:8792409/65‑1 (MQ=255)

                             gcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                    <  1:1269042/68‑1 (MQ=255)

                               gAGTTCTAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                   <  1:41290474/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                   <  1:55908349/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                   <  1:30890687/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                   <  1:18974881/67‑1 (MQ=255)

                               gAGTTCGAGCCGCGTTTCCCGCTCCAAAATTTGAAAGTGCTGGAAGGCACAGACCACCCAAGCGGGa                                   <  1:18098617/67‑1 (MQ=14)

                                  ttCGAGTCTCGTTTCCCGCGCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAg                               <  1:32461079/68‑1 (MQ=255)

                                   gcGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                              <  1:11646618/67‑1 (MQ=255)

                                       gTCTCGTTTCCCGGTAGAAAATTTTAAAGTTCTTTAAGGCACATACGACCCAAGCGGGAATAGCTCAg                          <  1:1566338/68‑1 (MQ=17)

                                       gTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCACGCGGGAATAGCTCa                           <  1:21535868/67‑1 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAACGCACAGACCACCCAAGCGGGAATAGCTCAGtt                        <  1:1399429/68‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                          <  1:10113157/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                          <  1:50884132/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                          <  1:29735793/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                          <  1:44155839/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                          <  1:35477778/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                          <  1:38829067/66‑1 (MQ=255)

                                         ctcGTTACCCGCTCCAAAATTTCAAAGTTCTGTAAGTCACAGACCACCCAAGCGGGAATAGCTCAg                          <  1:37747959/66‑1 (MQ=17)

                                         cgcGTTTCCCGCTCCAAAATATGAAAGTGCTGTAACGCACAGACCACCCAAGCGGGAATAGCTCAGtt                        <  1:3212732/66‑1 (MQ=14)

                                          tcGTTTCCCGCTCCAAAATTTTAAATTTCTGAAACGCACATACCACCCAAGCGGGAATAGCTCAGTTg                       <  1:40392159/68‑1 (MQ=14)

                                            gTTTCCCGCTACAAAATTTTAAAGTGCTGTACCGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                     <  1:11388357/68‑1 (MQ=14)

                                              ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTag                   >  1:45502486/1‑68 (MQ=255)

                                              ttCCCGCTCCAAAATTTGAAAGTGATGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGTTag                   >  1:48561668/1‑68 (MQ=255)

                                               tCCCGCCCCAAAATTTCAAAGTGCTGTAAGGCACAGACCACCCACGCGGGAATAGCTCAGTTGGTaga                  <  1:8323813/68‑1 (MQ=17)

                                                cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                  >  1:55280002/1‑67 (MQ=255)

                                                   gCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCAc              >  1:19844299/1‑68 (MQ=255)

                                                    cTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACg             >  1:9558304/1‑68 (MQ=255)

                                                      cgaaaaTTTTAAAGTGCTGTAAGTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc           <  1:33100259/66‑1 (MQ=17)

                                                      ccAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc           <  1:5259818/68‑1 (MQ=255)

                                                      ccAAAATCTAAAATTTCTGTAACACACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc           <  1:34365439/68‑1 (MQ=14)

                                                          aaTTTTAAATTGCTGTAAGTCACAGACGACCCACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg       <  1:46194545/68‑1 (MQ=14)

                                                           aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg       >  1:43372496/1‑67 (MQ=255)

                                                               gAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAg  <  1:29334919/68‑1 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAG  >  CP009273/4382308‑4382438

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: `‑`