BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,986,739	C→T	27.8%	Q743* (CAG→TAG)	cyaA →	adenylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,986,739	0	C	T	27.8%	569.5 / 298.2	356	Q743* (CAG→TAG)	cyaA	adenylate cyclase
Reads supporting (aligned to +/- strand): ref base C (107/150); new base T (33/66); total (140/216)
Fisher's exact test for biased strand distribution p-value = 1.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

Only 100 of 378 total aligned reads displayed.

GCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACC  >  CP009273/3986672‑3986805

gCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATcc                                                                    >  1:19250295/1‑68 (MQ=255)

gCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATcc                                                                    >  1:24583952/1‑68 (MQ=255)

gCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATcc                                                                    >  1:7858599/1‑68 (MQ=255)

gCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATcc                                                                    >  1:30201321/1‑68 (MQ=255)

gCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATcc                                                                    >  1:27202816/1‑68 (MQ=255)

 cAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCa                                                                   >  1:11887988/1‑68 (MQ=255)

 cAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGAGCATCCa                                                                   >  1:18246512/1‑68 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGt                                                                 >  1:29752845/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGt                                                                 >  1:1261594/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGt                                                                 >  1:7531545/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGt                                                                 >  1:27714687/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGt                                                                 <  1:28175730/66‑1 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGt                                                                 <  1:25314180/66‑1 (MQ=255)

         aaCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCttt                                                            <  1:7428360/67‑1 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCtttt                                                           >  1:17063655/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                           >  1:28058555/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                           >  1:4674636/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                           >  1:4487634/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                           >  1:12489985/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                           >  1:10945889/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                           >  1:8310759/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                           >  1:18022155/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTCCCAGCGAAGGGATCATCTAGTTCtttt                                                           >  1:4887373/1‑67 (MQ=255)

              aTCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCgaa                                                      >  1:23041778/1‑68 (MQ=255)

               tCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCgaag                                                     >  1:30747218/1‑68 (MQ=255)

               tCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCgaag                                                     >  1:13927581/1‑68 (MQ=255)

                   gTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAAc                                                 <  1:194879/68‑1 (MQ=255)

                   gTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAAc                                                 >  1:20902706/1‑68 (MQ=255)

                    tCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAAc                                                 >  1:29532525/1‑67 (MQ=255)

                     cAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACg                                                <  1:24913896/67‑1 (MQ=255)

                     cAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACg                                                <  1:26383017/67‑1 (MQ=255)

                      aaaTTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCa                                              <  1:9449849/68‑1 (MQ=255)

                        aTTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAg                                            <  1:4122242/68‑1 (MQ=255)

                        aTTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAg                                            <  1:22530590/68‑1 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAg                                            >  1:5443514/1‑67 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAg                                            >  1:2150897/1‑67 (MQ=255)

                           aCCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACg                                         <  1:28956590/68‑1 (MQ=255)

                           aCCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACg                                         <  1:5205623/68‑1 (MQ=255)

                            ccGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACga                                        <  1:1164975/68‑1 (MQ=255)

                             cggcggTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACgag                                       >  1:6487346/1‑68 (MQ=255)

                             cggcggTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACgag                                       <  1:28437834/68‑1 (MQ=255)

                              ggcggTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACgaga                                      >  1:14949774/1‑68 (MQ=255)

                                   tggtggACGGCTTTGCCCCCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATgg                                  <  1:21895764/67‑1 (MQ=255)

                                   tggtggACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATgg                                  <  1:12050858/67‑1 (MQ=255)

                                   tggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATgg                                  <  1:16838722/67‑1 (MQ=255)

                                   tggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATgg                                  <  1:31683470/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:22882316/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:22396135/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:21318737/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:18674903/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:5949374/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:30817285/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:1758884/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                 <  1:14518535/67‑1 (MQ=255)

                                      tggACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCtt                               <  1:20327936/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:10736165/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:3463434/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:16257235/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:27053167/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:20518204/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:27841321/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:25212609/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:31260940/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:15439945/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:2423019/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:7158684/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:31883880/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:10272737/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:10432898/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:14606758/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           >  1:25658469/1‑68 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                          <  1:32108300/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           <  1:8447939/67‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                          <  1:18481948/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                          <  1:9773970/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                          <  1:22164201/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                          <  1:30888860/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                           <  1:19037922/67‑1 (MQ=255)

                                            gCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                            <  1:15764099/64‑1 (MQ=255)

                                             cTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATc                        <  1:3862252/67‑1 (MQ=255)

                                              tttGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTTATATCt                       <  1:1121508/67‑1 (MQ=255)

                                              tttGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCt                       <  1:13092847/67‑1 (MQ=255)

                                                tGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACa                    <  1:2606500/68‑1 (MQ=255)

                                                  ccAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACAt                   >  1:20097716/1‑67 (MQ=255)

                                                  ccAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACAt                   >  1:29275586/1‑67 (MQ=255)

                                                   cAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACAt                   >  1:28668165/1‑66 (MQ=255)

                                                   cAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACAt                   >  1:29821955/1‑66 (MQ=255)

                                                   cAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACAt                   >  1:6214073/1‑66 (MQ=255)

                                                      cGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTcg              >  1:1424681/1‑68 (MQ=255)

                                                       gAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATtct                <  1:19360955/65‑1 (MQ=255)

                                                       gAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTcg              <  1:15327551/67‑1 (MQ=255)

                                                        aaGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTcgac            >  1:6846513/1‑68 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTcgacga          <  1:16726782/66‑1 (MQ=255)

                                                             atcatcTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa        <  1:26753085/67‑1 (MQ=255)

                                                             atcatcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa        <  1:10019629/67‑1 (MQ=255)

                                                             atcatcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa        <  1:22010355/67‑1 (MQ=255)

                                                              tcatcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGc      <  1:12788105/68‑1 (MQ=255)

                                                               catcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCa     <  1:8859848/68‑1 (MQ=255)

                                                                atcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCa     >  1:27452588/1‑67 (MQ=255)

                                                                  ccAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAAcc  >  1:3546139/1‑68 (MQ=255)

GCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACC  >  CP009273/3986672‑3986805

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: `‑`