BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	3,643,684	C→T	7.8%	S615S (TCG→TCA)	cyaA ←	adenylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	3,643,684	0	C	T	7.8%	319.2 / 11.2	102	S615S (TCG→TCA)	cyaA	adenylate cyclase
Reads supporting (aligned to +/- strand): ref base C (41/53); new base T (2/6); total (43/59)
Fisher's exact test for biased strand distribution p-value = 4.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 113 total aligned reads displayed.

CTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGCTA  >  AP009048/3643614‑3643753

cTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGatcatc                                                                       >  1:2414587/1‑71 (MQ=255)

   ccACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGa                                                                     <  1:968231/70‑1 (MQ=255)

   ccACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGAt                                                                    >  1:7568092/1‑71 (MQ=255)

   ccACGCTATCTGGAGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGatcatc                                                                       >  1:783914/1‑68 (MQ=255)

    cACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGAtt                                                                   >  1:6228778/1‑71 (MQ=255)

    cACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGAtt                                                                   >  1:6812709/1‑71 (MQ=255)

       gCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCt                                                                <  1:697719/71‑1 (MQ=255)

        cTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTc                                                               >  1:7305549/1‑71 (MQ=255)

          aTCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             >  1:6157881/1‑71 (MQ=255)

           tCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGcc                                                            >  1:4162584/1‑71 (MQ=255)

              ggCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGtt                                                         >  1:3503838/1‑71 (MQ=255)

              ggCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGtt                                                         >  1:4212808/1‑71 (MQ=255)

               gCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCATGGCTTCGATCATCGATTGCTCGCCGtt                                                         <  1:4673929/70‑1 (MQ=255)

               gCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGtt                                                         <  1:1939115/70‑1 (MQ=255)

               gCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGt                                                          <  1:6942221/69‑1 (MQ=255)

                cGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTg                                                        >  1:6697069/1‑70 (MQ=255)

                  gTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGaa                                                      <  1:6949865/70‑1 (MQ=255)

                   tGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTg                                                        <  1:580876/67‑1 (MQ=255)

                       gcgTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGt                                                          <  1:6529871/61‑1 (MQ=255)

                        cgTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGc                                               >  1:1098590/1‑71 (MQ=255)

                         gTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             <  1:6794908/56‑1 (MQ=255)

                         gTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             <  1:1174107/56‑1 (MQ=255)

                         gTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCg                                              <  1:5728191/71‑1 (MQ=255)

                          tCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTg                                                   <  1:7898013/65‑1 (MQ=255)

                           ccTGATGCATTTTGCCGAGAATAGTTTTCAGTGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTa                                            >  1:2459836/1‑71 (MQ=255)

                           ccTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTa                                            >  1:2471569/1‑71 (MQ=255)

                           acTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTa                                            >  1:5459971/2‑71 (MQ=255)

                             tGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAg                                                     >  1:3953231/1‑60 (MQ=255)

                                  cATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTg                                                        <  1:3851540/52‑1 (MQ=255)

                                  cATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACtt                                     >  1:4118874/1‑71 (MQ=255)

                                    ttttGCCGAGAATAGTTTTCATGGCTTCGatcatc                                                                       <  1:87046/35‑1 (MQ=255)

                                    ttttGCCGAGAATAGTTTTCAGGGCTTCGatcatc                                                                       <  1:5473066/35‑1 (MQ=255)

                                    ttttGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCGGCGTACGCACTTCg                                   <  1:2366497/71‑1 (MQ=255)

                                      ttGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGtt                                 >  1:7685988/1‑71 (MQ=255)

                                       tGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGtt                                 <  1:5404765/70‑1 (MQ=255)

                                        gCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGc                                                                 >  1:6517291/1‑37 (MQ=255)

                                        gCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             >  1:4386516/1‑41 (MQ=255)

                                        gCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGtt                                 <  1:7011444/69‑1 (MQ=255)

                                        gCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTc                                >  1:533141/1‑70 (MQ=255)

                                         ccGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGt                                                          <  1:5944901/43‑1 (MQ=255)

                                         ccGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTc                                <  1:7629455/69‑1 (MQ=255)

                                         ccGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTc                                <  1:5109020/69‑1 (MQ=255)

                                          cGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             <  1:4269668/39‑1 (MQ=255)

                                          cGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             <  1:5522095/39‑1 (MQ=255)

                                          cGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             <  1:7338054/39‑1 (MQ=255)

                                          cGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGc                                                             <  1:454005/39‑1 (MQ=255)

                                           gagaATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGGTCCACg                            <  1:1026683/71‑1 (MQ=255)

                                            agaATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCa                                        >  1:5862374/1‑58 (MQ=255)

                                            agaATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCa                                        >  1:1352915/1‑58 (MQ=255)

                                            agaATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCAc                             >  1:3626288/1‑69 (MQ=255)

                                            agaATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCAc                             >  1:4390702/1‑69 (MQ=255)

                                            agaATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCAc                             >  1:583290/1‑69 (MQ=255)

                                               aTAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCa                                        >  1:4771426/1‑55 (MQ=255)

                                               aTAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCa                                        >  1:1268937/1‑55 (MQ=255)

                                               aTAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGtt                        >  1:1291519/1‑71 (MQ=255)

                                               aTAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGtt                        >  1:6306539/1‑71 (MQ=255)

                                                tAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCa                                                 >  1:6998932/1‑45 (MQ=255)

                                                tAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCa                                                 >  1:4286999/1‑45 (MQ=255)

                                                tAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCg                                              <  1:5608378/48‑1 (MQ=255)

                                                tAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTcc                               <  1:1729688/63‑1 (MQ=255)

                                                tAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTg                       <  1:7108522/71‑1 (MQ=255)

                                                tAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTg                       <  1:3932075/71‑1 (MQ=255)

                                                  gTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGc                      <  1:2978781/70‑1 (MQ=255)

                                                  gTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCg                     <  1:71198/71‑1 (MQ=255)

                                                   ttttCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACg                            <  1:2648969/63‑1 (MQ=255)

                                                   ttttCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGc                      <  1:5041765/69‑1 (MQ=255)

                                                     ttCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTa                  >  1:4338864/1‑71 (MQ=255)

                                                      tCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTa                  <  1:5271469/70‑1 (MQ=255)

                                                      tCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTa                  <  1:4406604/70‑1 (MQ=255)

                                                        aGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               <  1:4884602/71‑1 (MQ=255)

                                                        aGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               <  1:6775596/71‑1 (MQ=255)

                                                        aGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAca                <  1:5221824/70‑1 (MQ=255)

                                                         gggCTTCGATCATCGATTGCTCGCCGTTGATGTGc                                                  <  1:3517165/35‑1 (MQ=255)

                                                         gggCTTCGATCATCGATTGCTCGCCGTTGAAGTGc                                                  <  1:5913735/35‑1 (MQ=255)

                                                         gggCTTCGATCATCGATTGCTCGCCGTTGAAGTGc                                                  <  1:4138153/35‑1 (MQ=255)

                                                         gggCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcagc              <  1:369800/71‑1 (MQ=255)

                                                         gggCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               <  1:2812998/70‑1 (MQ=255)

                                                          ggCTTCGATCATTGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTc                                    <  1:227597/48‑1 (MQ=255)

                                                          ggCTTCGATCATTGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTc                                    <  1:5149219/48‑1 (MQ=255)

                                                          ggCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               >  1:3476665/1‑69 (MQ=255)

                                                          ggCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               >  1:1083144/1‑69 (MQ=255)

                                                          ggCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               >  1:2494864/1‑69 (MQ=255)

                                                           gCTTCGATCATTGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTc                                    <  1:1586116/47‑1 (MQ=255)

                                                           gCTTCGATCATTGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTc                                    <  1:5791369/47‑1 (MQ=255)

                                                           gCTTCGATCATTGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTc                                    <  1:7012007/47‑1 (MQ=255)

                                                           gCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcagcag            >  1:448503/1‑71 (MQ=255)

                                                            cTTCGATCATTGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGt                                  >  1:5352645/1‑48 (MQ=255)

                                                            cTTCGATCATTGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGt                                  >  1:478436/1‑48 (MQ=255)

                                                              tCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAca                <  1:7444856/64‑1 (MQ=255)

                                                              tCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAca                <  1:2241744/64‑1 (MQ=255)

                                                               cGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               <  1:3506488/64‑1 (MQ=255)

                                                               cGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGt          <  1:2521279/69‑1 (MQ=255)

                                                                gATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCa        <  1:5897634/70‑1 (MQ=255)

                                                                 atcatcGATTGCTCGCCGTTGAAGAGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcagca             <  1:2542630/64‑1 (MQ=255)

                                                                  tcatcGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAg                          >  1:3916873/1‑50 (MQ=255)

                                                                   catcGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGc    >  1:7257981/1‑71 (MQ=255)

                                                                     tcGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTAcag               <  1:1913620/58‑1 (MQ=255)

                                                                     tcGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGcta  >  1:6041693/1‑71 (MQ=255)

                                                                     tcGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGcta  <  1:1695617/71‑1 (MQ=255)

                                                                     tcGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGcta  >  1:1050087/1‑71 (MQ=255)

CTTCCACGCTATCTGGCGGTGCGGCGTCCTGATGCATTTTGCCGAGAATAGTTTTCAGGGCTTCGATCATCGATTGCTCGCCGTTGAAGTGCAGCGTACGCACTTCGTTCCACGAGTTGCGGTACAGCAGGTCAACGCTA  >  AP009048/3643614‑3643753

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`