BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,596,005	T→A	6.3%	intergenic (‑23/+12)	leuV ← / ← leuP	tRNA‑Leu/tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,596,005	0	T	A	6.3%	972.7 / 7.8	344	intergenic (‑23/+12)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base T (153/166); new base A (2/23); total (155/189)
Fisher's exact test for biased strand distribution p-value = 8.22e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 356 total aligned reads displayed.

ACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAA  >  CP009273/4595938‑4596071

acTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGat                                                                     >  1:14674289/1‑68 (MQ=255)

    acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATc                                                                  >  1:17456452/1‑67 (MQ=255)

    acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATc                                                                  >  1:10748190/1‑67 (MQ=255)

    acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                                 <  1:7488778/68‑1 (MQ=255)

     cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                                <  1:24197170/68‑1 (MQ=255)

     cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                                <  1:11568938/68‑1 (MQ=255)

        cTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCCGCTGACTTTTTTTGATATCGCGTc                                                             >  1:10151144/1‑68 (MQ=18)

        cTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAGCTGACTTTTTTTGATATCGCCTc                                                             >  1:25211256/1‑68 (MQ=255)

         tGATGCTAGCGCGTCTACCATTTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                            <  1:24366390/68‑1 (MQ=255)

         tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                            <  1:3744530/68‑1 (MQ=255)

         tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                            <  1:27292396/68‑1 (MQ=255)

         tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                            <  1:10896508/68‑1 (MQ=255)

          gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTTATATCGCCTCGt                                                           <  1:31267791/68‑1 (MQ=255)

          gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGt                                                           <  1:20426971/68‑1 (MQ=255)

          gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGt                                                           <  1:6907779/68‑1 (MQ=255)

            aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGtt                                                          <  1:8882322/67‑1 (MQ=255)

            aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATAGCCGCGgtt                                                         >  1:15669685/1‑68 (MQ=21)

            aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCATACTTTTTTTGATATCGCCTCGtt                                                          <  1:5760791/67‑1 (MQ=255)

               tAGCGCGTCTACCAATTCCGCCAGCTTCGCACAGGCATCTTACTTTTTTTGATAGCGCCTCGTTTGGt                                                      <  1:31824412/68‑1 (MQ=37)

               tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                                       <  1:27056230/67‑1 (MQ=255)

               tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                      <  1:19596055/68‑1 (MQ=255)

               tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                      <  1:16760239/68‑1 (MQ=255)

               tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                      <  1:17661272/68‑1 (MQ=255)

               tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                      <  1:24756451/68‑1 (MQ=255)

               tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                      <  1:14374862/68‑1 (MQ=255)

               tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                      <  1:12205882/68‑1 (MQ=255)

                aGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTg                                                     <  1:327266/68‑1 (MQ=255)

                   gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGa                                                  <  1:5322028/68‑1 (MQ=255)

                   gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATAGCGTCGTTTGGTGCGa                                                  >  1:22047281/1‑68 (MQ=255)

                           cAATTCCGCCACCTTCGCACAGTCATCTTACTATCATTGCAATCGCCTCGTTTGGTGCGA‑ggggggg                                          >  1:11363945/1‑67 (MQ=37)

                            caTTCCGCCACCTACCCACAGGCAAGTTACATTTTTTGATATCTCCTCCTTTGGTGCGA‑GGGGGGGGa                                        <  1:33660826/67‑1 (MQ=19)

                            aaTTCCGGCACCTTCTCACAGTCATCTAACATTTTTTGAAATCGCCTCTTTTGGTGCGA‑GGGGGGGGa                                        <  1:8487255/68‑1 (MQ=37)

                            aaTTCCGCCACCTTCGCACCGTCATCTTACTTTTTTTGCTATCGCCTCGTTTGGTGCGA‑GGGGGGGGa                                        <  1:16285910/68‑1 (MQ=39)

                            aaTTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGa                                        <  1:4908110/68‑1 (MQ=255)

                             aTTCAGCCACCATATCACATTGATCTTACTTTTAATGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGAc                                       <  1:20169813/68‑1 (MQ=16)

                               tCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACtt                                     >  1:25721250/1‑68 (MQ=255)

                               tCCGCCACCTTAGCACATTCATCTAACTTTTTTTGATATCGCCACGTTTGGTGCGA‑GGGGGGGGACtt                                     <  1:18826018/68‑1 (MQ=37)

                                    cACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                                <  1:26406642/68‑1 (MQ=255)

                                    cACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCATCGTTTGGTGAGA‑GGGGGGGGACTTGAAc                                 >  1:8171322/1‑67 (MQ=255)

                                    cACCTTCCCACATTCATCAAACTTTTATTGATATAGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                                <  1:33400729/68‑1 (MQ=21)

                                     aacTTCCCACACTCAACTTACTTTTTTTGATTTCGCCACGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                               <  1:33949318/66‑1 (MQ=21)

                                     aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGAGTTGAAcc                                >  1:4591445/1‑67 (MQ=255)

                                     aCCTTCGCACAGGCATCTAACATTATTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                               <  1:9203722/68‑1 (MQ=25)

                                     aCCTTATCACATTCATCTTACTTTTTTTGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAAccc                               <  1:18482395/68‑1 (MQ=21)

                                      ccTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                               >  1:18021770/1‑67 (MQ=255)

                                      ccTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                               >  1:16482104/1‑67 (MQ=255)

                                           tcacaGGCATCTAACTTTTTTTGATATCGCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt                         <  1:2554681/67‑1 (MQ=21)

                                            cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt                         >  1:15316592/1‑67 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGCCTTGAACCACCACGTcc                       >  1:10355674/1‑68 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       >  1:26526462/1‑68 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       >  1:21501744/1‑68 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       >  1:23921798/1‑68 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       <  1:23471879/68‑1 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       >  1:27864119/1‑68 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       >  1:30033807/1‑68 (MQ=255)

                                             acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       >  1:23713816/1‑68 (MQ=255)

                                             acaGTCATCAAACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                       <  1:28302262/68‑1 (MQ=255)

                                              caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg                      >  1:6377158/1‑68 (MQ=255)

                                               aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGt                     >  1:13411294/1‑68 (MQ=255)

                                               aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGt                     >  1:32159237/1‑68 (MQ=255)

                                                gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa                    >  1:23647366/1‑68 (MQ=255)

                                                cgcATCTAACAATTATTGATATAGCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa                    <  1:20879558/66‑1 (MQ=14)

                                                 tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTaa                   >  1:30936320/1‑68 (MQ=255)

                                                  gaTCTTACATTTATTGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg                      <  1:5428686/63‑1 (MQ=17)

                                                  catcatACTTTTTTTGATATCCCCTATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg                      <  1:5169700/64‑1 (MQ=18)

                                                  cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg                      <  1:20653170/64‑1 (MQ=255)

                                                  cATCTTAATTTTTTTTATATCGCCTGGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg                      <  1:30672210/64‑1 (MQ=18)

                                                     cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:31605323/1‑68 (MQ=255)

                                                     cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:21085789/1‑68 (MQ=255)

                                                     cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:2163685/1‑68 (MQ=255)

                                                      ttACTTTTTTTGATATCTCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca              <  1:22913646/68‑1 (MQ=255)

                                                      atACTATATTGGATCTCCCCTCGATTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca              <  1:30199510/67‑1 (MQ=14)

                                                       tACTTTTTTTGATCTCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTTAACCCCCACGTCCGTAAGAacac             <  1:27607102/68‑1 (MQ=21)

                                                       tACTTTTTTTGATATCGCCTCGTTTTGTGCGA‑GGGGGGGGACTTGAACCCCCACGGCCGTAAGAac               >  1:29759630/1‑66 (MQ=25)

                                                       tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGaaagc             >  1:34463033/1‑65 (MQ=255)

                                                       tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAacac             >  1:34153423/1‑68 (MQ=255)

                                                       tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:25795168/1‑66 (MQ=255)

                                                       tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:7699788/1‑66 (MQ=255)

                                                       tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:16158823/1‑66 (MQ=255)

                                                       tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:26006424/1‑66 (MQ=255)

                                                       tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac               >  1:29642191/1‑66 (MQ=255)

                                                        aCTTTTTTTGATCTCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACt            <  1:310886/68‑1 (MQ=255)

                                                         cTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:24557150/1‑68 (MQ=255)

                                                         cTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:2854154/1‑68 (MQ=255)

                                                         cTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:31479718/1‑68 (MQ=255)

                                                         cTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:1642978/1‑68 (MQ=255)

                                                          tttttttGATATCGCCTCGTTTGCTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa           >  1:29306428/1‑67 (MQ=255)

                                                            tttttGATATCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        <  1:19857021/68‑1 (MQ=255)

                                                            tttttGATATCCCCTATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        <  1:19154631/68‑1 (MQ=17)

                                                            tttttGAAATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        <  1:33603749/68‑1 (MQ=255)

                                                            tttttGAAAACGCCAGTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        <  1:1200300/68‑1 (MQ=11)

                                                            ttattGATATAGCCTGTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca        <  1:32340426/65‑1 (MQ=14)

                                                            tatttGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAaca        <  1:17051474/66‑1 (MQ=14)

                                                              tttGATATCTCCTATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc      <  1:6680325/68‑1 (MQ=14)

                                                              tttGATATCGCCTATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc      <  1:12845921/68‑1 (MQ=255)

                                                              tttGAAATCTCCACTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc      <  1:32926835/68‑1 (MQ=14)

                                                              attGATATATCCTCTTTTTGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc      <  1:7384213/67‑1 (MQ=14)

                                                                  atatCGCCTCGTTTGGTGCGAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGa   >  1:4391630/1‑68 (MQ=255)

                                                                   tatCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa  <  1:9492295/67‑1 (MQ=255)

                                                                   tatCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa  >  1:6606217/1‑67 (MQ=255)

ACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAA  >  CP009273/4595938‑4596071

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: `‑`