BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,282,813	T→A	5.4%	intergenic (‑29/+181)	tyrV ← / ← tyrT	tRNA‑Tyr/tRNA‑Tyr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,282,813	0	T	A	5.4%	2644.3 / 17.5	918	intergenic (‑29/+181)	tyrV/tyrT	tRNA‑Tyr/tRNA‑Tyr
Reads supporting (aligned to +/- strand): ref base T (417/417); new base A (15/41); total (459/459)
Fisher's exact test for biased strand distribution p-value = 8.08e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 954 total aligned reads displayed.

TTTACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCTGTGGC  >  CP009273/1282746‑1282880

 ttACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCtt                                                                    <  1:20952718/68‑1 (MQ=255)

  tACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTg                                                                   >  1:1091243/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                                >  1:8820188/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                                >  1:16393756/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                                >  1:3706370/1‑68 (MQ=255)

     aGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTAAAATTTTGAGGTAATGCTTgaga                                                                >  1:20789793/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtg                                                              >  1:5660320/1‑68 (MQ=255)

       tCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtg                                                              >  1:3592169/1‑68 (MQ=255)

        cTGCTCCCTTTGGCCGCTTGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtgg                                                             <  1:6956062/68‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgaga                                                                <  1:13438146/65‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                                 <  1:24418179/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                                 <  1:18862941/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                                 <  1:21857620/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                                 <  1:14929109/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                                 <  1:32478020/64‑1 (MQ=255)

        cTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTgag                                                                 <  1:9634538/64‑1 (MQ=255)

         tGCTCCCTTTGGCCGGTAGGGAACCCCACCAGTGGTAATTCAAATTTTGAGGTAATGCTTGAGAttgt                                                            <  1:1728571/68‑1 (MQ=37)

         tGCTCCCTTTGGCCGCTCGGTAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:32035914/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGTGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:12085317/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:4266553/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:2331324/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:25159306/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:28662589/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:21293100/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:31539450/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:30848011/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:1962012/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:5194735/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:1299889/68‑1 (MQ=255)

         tGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggt                                                            <  1:15205449/68‑1 (MQ=255)

          gCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggtg                                                           >  1:19145618/1‑68 (MQ=255)

            tCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggtgg                                                          <  1:9179746/67‑1 (MQ=255)

             cccTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGAtggtggtg                                                        >  1:16610689/1‑68 (MQ=255)

             cccTTTGGCCGCTCGGGAACCCCACCAGGGGGTATTCAAATTTTGAGGTAAGCCGTGAGAtggtggtg                                                        >  1:2962638/1‑68 (MQ=21)

               cTTTGGCCGCTCGGGAACCCCACCAGGGGTTAATCAAGTTTACAGGTATTGGGTGTGAtggtggtgcg                                                      >  1:35432815/1‑66 (MQ=12)

               cTTTGGCCGATCTGGAACCCCACCAGGGGTAATTCAAATTTTGCTGTAATGCTTGAGATGGTGGTggg                                                      <  1:23811494/68‑1 (MQ=38)

               cTTTGGCCGATCAGTAACCCCACCAGGGGTTTTTCAAATTTTGAGGTAATGCTTGAGATGGTGGTggg                                                      <  1:18421636/68‑1 (MQ=255)

                tttGGCCGCTCGTTAACCTGACCATGGGTAATTCAAATTTTGTGGTATTGCTTGAGATGGTGGTgggg                                                     <  1:15749960/68‑1 (MQ=255)

                tttGGCCGCTCGGTAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTgggg                                                     <  1:16071637/68‑1 (MQ=255)

                tttGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTgggg                                                     <  1:2717854/68‑1 (MQ=255)

                tttGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGATTGAGATGGTGGTgggg                                                     <  1:13704557/68‑1 (MQ=255)

                 ttGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTggggg                                                    >  1:6251944/1‑68 (MQ=255)

                 ttGGCCGCTCGGGAACCCCACCAGGGGGAATTCATTTTTAGAGGCATGCCAGGAGATCGTGGTgggg                                                     >  1:34607706/1‑67 (MQ=9)

                    gCCGCTCGGGAACCCCACCAGGGGTTAATCATTTTTTGAGGAATTGCAGGAGATGGTGGTGCGGGAAg                                                 >  1:34132428/1‑68 (MQ=16)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCATTTTTTGAGGTATTGGGTGAGATGGTGGGGGGGGAAg                                                 >  1:12371677/1‑68 (MQ=25)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                                 >  1:15467507/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAg                                                 >  1:7307641/1‑68 (MQ=255)

                    gCCGCTCGGGAACCCCACCAGGGGTAAATCAATTTTTCTGGAAATCATCGTGATCGTGGAGGGGGAAg                                                 >  1:798017/1‑68 (MQ=12)

                    gCCGCTCGGGAACCCCACAACGGGTAAATCAATTTTTCAGGTATTCCATGAGATGGGGGTGGGGGGAg                                                 >  1:17982293/1‑68 (MQ=16)

                     ccGCTCGGTAACTTCCCCAGGGGTAAAAGATATTTTGTGGTAATGCATGAGATGGTGGTGGGGGAAgg                                                <  1:20192563/68‑1 (MQ=255)

                      cGCTCTGTAACCCGACCATGGGTTATTCAAATTATGAGGTAATGCATGAGATGGTGGTGGGGGAAgg                                                <  1:36179405/67‑1 (MQ=255)

                      cGCTCGGTACCCCCACCAGGGGTAATTCAAATTTTGTGGTAATGCTTGAGATGGTGGTGGGGGAAgg                                                <  1:36793121/67‑1 (MQ=255)

                      cGCTAGGGAACACCCCCAGGGGTAATTCAAATTATGAGGTTATGCTTGAGATGGTGGTGGGGGAAgg                                                <  1:2935608/67‑1 (MQ=255)

                         tCGGGAACCCCACCAGGGGTAATTCATTTTTTGAGGTATTCAGGGTGATGGTGGTGGGGGAAGGatta                                            >  1:3937083/1‑68 (MQ=21)

                          ctggAACCCCACCAGGGGTAATTCAAATTTTGTGGTAATGCTTGAGATGGTGGTGGGGGAAGGattat                                           <  1:33685069/66‑1 (MQ=255)

                               aCCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                      >  1:12674847/1‑68 (MQ=255)

                               aCCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                      >  1:21566712/1‑68 (MQ=255)

                               aCCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATtcgtc                                      >  1:30525228/1‑68 (MQ=255)

                               aCCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGGGGTGGGGGAAGCATTATtcgtc                                      >  1:11340611/1‑68 (MQ=255)

                               aCCCCACCAGGGGTAATTCAAATTTTGAGGAAATGCTTGTGATGGTGGTGGGGGAAGGATTATtagta                                      >  1:30342448/1‑67 (MQ=37)

                                 cccACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATtcgta                                      >  1:27705201/1‑65 (MQ=255)

                                 cccACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATtagtc                                      >  1:25941460/1‑66 (MQ=255)

                                 cccACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATacgtc                                      >  1:26206823/1‑66 (MQ=255)

                                      caGGGGTAATTCAAATTTTGCCGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                               <  1:10317449/68‑1 (MQ=255)

                                      caGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttc                                 >  1:32869800/1‑66 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                               >  1:29862288/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                               >  1:22241644/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                               >  1:12792896/1‑67 (MQ=255)

                                       aGGGGTAATTCAAATTTTGAGGGAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgc                               >  1:6541983/1‑67 (MQ=255)

                                         gggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                              >  1:16834449/1‑66 (MQ=255)

                                          ggTAATTCAAATTTTGCGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                              <  1:1064216/65‑1 (MQ=255)

                                          ggTAATTCAAATTTTGATGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                            <  1:8532462/67‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGtcgcttcgct                              <  1:17567893/65‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                            >  1:2836668/1‑67 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                            >  1:7780579/1‑67 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                            >  1:28868898/1‑67 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcc                            <  1:4473387/67‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctc                             <  1:24746578/66‑1 (MQ=255)

                                          ggTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctc                             <  1:14184809/66‑1 (MQ=255)

                                          ggTAATACAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATAATTCGACGCTTCGctcc                            >  1:25489464/1‑67 (MQ=38)

                                            tttttCAAATTTGGCGGTTATGATTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                          <  1:36353643/64‑1 (MQ=37)

                                            tAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGctcctc                          >  1:30196772/1‑67 (MQ=255)

                                            tAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGatcctc                          >  1:4803211/1‑67 (MQ=255)

                                               ttCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCAc                        >  1:22826756/1‑66 (MQ=255)

                                               ttCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCAc                        >  1:1464229/1‑66 (MQ=255)

                                                tCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCt                     >  1:3336218/1‑68 (MQ=255)

                                                tCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTAGTCGCTTCGCTCCTCACCCt                     >  1:34959366/1‑68 (MQ=255)

                                                      tttGTGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGc               <  1:27486451/68‑1 (MQ=255)

                                                           ggTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGtt           >  1:10021791/1‑67 (MQ=255)

                                                           ggTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGtt           >  1:35171795/1‑67 (MQ=255)

                                                            gTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTg          >  1:6672683/1‑67 (MQ=255)

                                                            gTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTg          >  1:14359669/1‑67 (MQ=255)

                                                            gTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTg          >  1:7498928/1‑67 (MQ=255)

                                                            gTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTg          >  1:8265645/1‑67 (MQ=255)

                                                            ctAATGAATGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGc         <  1:28037564/67‑1 (MQ=25)

                                                             tAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGc         <  1:11825389/67‑1 (MQ=255)

                                                                 gCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCtgtg    >  1:22577999/1‑68 (MQ=255)

                                                                  cTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCtgtg    >  1:20606274/1‑67 (MQ=255)

                                                                   ttGTGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCTGTGGc  <  1:26828883/68‑1 (MQ=255)

                                                                   ttGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTAGCTCCTCACCCTTCGTGCCGTTGCCTGTGGc  >  1:2663014/1‑68 (MQ=255)

TTTACAGTCTGCTCCCTTTGGCCGCTCGGGAACCCCACCAGGGGTAATTCAAATTTTGAGGTAATGCTTGAGATGGTGGTGGGGGAAGGATTATTCGTCGCTTCGCTCCTCACCCTTCGGGCCGTTGCCTGTGGC  >  CP009273/1282746‑1282880

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: `‑`