BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,282,812	C→A	5.7%	intergenic (‑28/+182)	tyrV ← / ← tyrT	tRNA‑Tyr/tRNA‑Tyr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,282,812	0	C	A	5.7%	1790.6 / 9.9	604	intergenic (‑28/+182)	tyrV/tyrT	tRNA‑Tyr/tRNA‑Tyr
Reads supporting (aligned to +/- strand): ref base C (277/265); new base A (13/32); total (307/297)
Fisher's exact test for biased strand distribution p-value = 4.88e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 633 total aligned reads displayed.

TTTACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCTGTG  >  CP009273/1282746‑1282878

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                     <  1:7731146/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                     <  1:26753222/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                     <  1:23250905/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGc                                                                     <  1:15925930/67‑1 (MQ=255)

tttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑t                                                                   >  1:1007174/1‑68 (MQ=255)

 ttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑tt                                                                  <  1:50916214/68‑1 (MQ=255)

  tACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTg                                                                 >  1:55517540/1‑68 (MQ=255)

  tACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTg                                                                 <  1:15129380/68‑1 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgaga                                                              >  1:9509361/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgaga                                                              >  1:1748547/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTGAAATTTTGAGGGAAGGC‑TTGAGAtg                                                            >  1:46101458/1‑68 (MQ=21)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtg                                                            >  1:37563595/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtg                                                            >  1:20504930/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAAGGG‑TTGAGAtg                                                            >  1:36238775/1‑68 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGTGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgag                                                               <  1:30132320/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgag                                                               <  1:186714/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgag                                                               <  1:43702223/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgag                                                               <  1:49114520/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgag                                                               <  1:33853763/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgag                                                               <  1:36849556/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTgag                                                               <  1:38001372/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtgg                                                           <  1:51651404/68‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtgg                                                           <  1:57560162/68‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtgg                                                           <  1:45170312/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggt                                                          <  1:50525910/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggt                                                          <  1:14033950/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggt                                                          <  1:33545269/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggt                                                          <  1:47555181/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggt                                                          <  1:55004455/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggt                                                          <  1:56402600/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggt                                                          <  1:19733440/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTCTGAGGTAATGC‑TTGAGAtggt                                                          <  1:53674586/68‑1 (MQ=255)

          gCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggtg                                                         >  1:32157776/1‑68 (MQ=255)

          gCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggtg                                                         <  1:42387794/68‑1 (MQ=255)

            tCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggtgg                                                        <  1:27950670/67‑1 (MQ=255)

            tCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggtgg                                                        <  1:5325799/67‑1 (MQ=255)

             cccTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCCAATTTTCAGGAAATGA‑GAGAGAtggtggt                                                       >  1:41029757/1‑67 (MQ=18)

             cccTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggtggtg                                                      >  1:1319643/1‑68 (MQ=255)

             cccTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGAtggtggtg                                                      >  1:25721464/1‑68 (MQ=255)

               cTTTGGCCGCTCTGGAACCCCACCAGTGGTAATTCATATTTTGAGGTAATGC‑TTGAGATGGTGGTggg                                                    <  1:3468483/68‑1 (MQ=38)

               cTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTACAGGGAATCG‑GTGTGATGGGGGTggg                                                    >  1:10529730/1‑68 (MQ=18)

               cTTTGGCCGCTCGGGAACCCCACAAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTggg                                                    >  1:16632921/1‑68 (MQ=255)

                tttGGGCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTgggg                                                   <  1:24554159/68‑1 (MQ=255)

                tttGGCCGCTCGGTAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTgggg                                                   <  1:41655158/68‑1 (MQ=255)

                 ttGGCCGCTCGGGAACCCGACAAGGGGAAAATAAAAATTTGAGGTAAGAC‑ATGAGATGGTGGTggggg                                                  >  1:58012942/1‑68 (MQ=255)

                 ttGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTggggg                                                  >  1:23745668/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTTATTCATTTTTTGAGGGAATGC‑TGGATATGGTGTTGCGGGAAg                                               >  1:2078037/1‑68 (MQ=21)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCATATTTTGAGGTAATGC‑ATGAGATGGTGTTGGGGGAAg                                               >  1:31533339/1‑68 (MQ=38)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAg                                               >  1:54024112/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAg                                               >  1:29654777/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAg                                               >  1:44620216/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAg                                               >  1:48900978/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAg                                               >  1:11736665/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAg                                               >  1:6868328/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAg                                               >  1:7182277/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGGAATTCCAATTTAGAGGT‑ATGCATTGATATGGGGGTGGGGGCAg                                               >  1:21938731/1‑68 (MQ=16)

                    gCCGCTCGGGAACCCCACCACGGGTAATTCAAATTTTGTGGGAATGC‑AAGAGATGGTGTTGGGGGaa                                                >  1:25924521/1‑67 (MQ=25)

                      cGCTCTTGAACCGCCGCAGTGGTAATTCATTTTTTGATCTAATGA‑TTGAGATGGTGGTGGGGGAAgg                                              <  1:38780185/67‑1 (MQ=255)

                      cGCTCGTGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAgg                                              <  1:20262612/67‑1 (MQ=255)

                      cGCCCGGGAACCCCCGCAGGGGTATTTCATCTTTTGCGGTAATGC‑TTGAGATGGTGGTGGGGGAAgg                                              <  1:6654808/67‑1 (MQ=255)

                         tCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGatt                                           <  1:50018935/67‑1 (MQ=255)

                           gggAACCCCACCAGGGGTATTGCAAATTTTGAGGTATTGC‑TTGAGATGGTGGTGGGGGAAGGattatt                                        <  1:41226922/68‑1 (MQ=38)

                               aCCCCACCAGGGGTAATTGAATTTTTGTGGTATTGC‑TAGAGATGGTGGTGGGGGCAGGATTATtcgtc                                    >  1:39427710/1‑68 (MQ=37)

                               aCCCCACCAGGGGTAATTCAAATTTTGTGGTAATGC‑GGGAGATGGTGGTGCGGGAAGGATTATtcgtc                                    >  1:6088365/1‑68 (MQ=38)

                               aCCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                    >  1:2630781/1‑68 (MQ=255)

                               aCCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                    >  1:35012660/1‑68 (MQ=255)

                                 cccACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                    >  1:3255767/1‑66 (MQ=255)

                                  ccaccaGGGGTAATTCATATATTGCCGTAATGC‑TAGAGATGGTGGTGGGGGAAGGATTATTCGtcgct                                 <  1:46703407/68‑1 (MQ=37)

                                  ccaccaGGGGTAATTCAAATTTTGCGCTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgct                                 <  1:18244940/68‑1 (MQ=255)

                                     gcaGGGGTATTTAATATATTGAGGTATTGA‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttc                               <  1:8852874/66‑1 (MQ=25)

                                     ccaGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttc                               >  1:56937576/1‑67 (MQ=255)

                                     ccaGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttc                               >  1:35828972/1‑67 (MQ=255)

                                     ccaGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgctac                               >  1:19312031/1‑65 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                             >  1:11307884/1‑67 (MQ=255)

                                         gggTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            >  1:27459453/1‑66 (MQ=255)

                                         gggTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            >  1:39852852/1‑66 (MQ=255)

                                          tgTAATACAAATTTTTTTGTTATGC‑AAGCGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                          <  1:4705669/66‑1 (MQ=16)

                                          ggTATTTCAAATTTTGAGCTCATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcct                         <  1:28660954/68‑1 (MQ=38)

                                          ggTAATTCAAATTTTGAGGTAATGC‑TTGTGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            <  1:2263572/65‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            <  1:34262399/65‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                          >  1:32819588/1‑67 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                          >  1:40416040/1‑67 (MQ=255)

                                          cgTAATTCAAATATTGACGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                            <  1:45585972/64‑1 (MQ=38)

                                           gTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        >  1:52654075/1‑68 (MQ=255)

                                           gTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        >  1:13572885/1‑68 (MQ=255)

                                            tttttCATATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        <  1:30960625/64‑1 (MQ=255)

                                            tAATTCACATAATGACGTAATGC‑ATGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        <  1:214997/67‑1 (MQ=37)

                                            tAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        >  1:48605854/1‑67 (MQ=255)

                                            tAATTCAAATTATGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                        <  1:12425375/67‑1 (MQ=255)

                                              aTTCAAATTTTGTTGTATTGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCAcc                     <  1:52330146/68‑1 (MQ=38)

                                               ttCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCAccc                    <  1:10865012/68‑1 (MQ=255)

                                               ttCAAATTTTGAGGTAATGA‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCAccc                    <  1:843092/68‑1 (MQ=255)

                                                tCAATTTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCt                   <  1:43278605/68‑1 (MQ=255)

                                                tCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCt                   <  1:31709058/68‑1 (MQ=255)

                                                tCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCt                   >  1:42828827/1‑68 (MQ=255)

                                                tCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCt                   >  1:1460511/1‑68 (MQ=255)

                                                           ggTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGtt         >  1:35401190/1‑67 (MQ=255)

                                                             tAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGc       <  1:54461715/67‑1 (MQ=255)

                                                              aaTGC‑TAGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCt     <  1:12115013/68‑1 (MQ=255)

                                                                 gC‑TAGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCtgtg  <  1:4583224/68‑1 (MQ=255)

TTTACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGC‑TTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCTGTG  >  CP009273/1282746‑1282878

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: `‑`