BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,986,739	C→T	5.4%	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	5.4%	1335.8 / 46.2	405	Q743* (CAG→TAG)	cyaA	adenylate cyclase
Reads supporting (aligned to +/- strand): ref base C (143/239); new base T (12/10); total (155/250)
Fisher's exact test for biased strand distribution p-value = 1.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.92e-01

Only 100 of 432 total aligned reads displayed.

GCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCG  >  CP009273/3986672‑3986806

gCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATcc                                                                     >  1:17817838/1‑68 (MQ=255)

gCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATcc                                                                     >  1:4545476/1‑68 (MQ=255)

 cAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCa                                                                    >  1:592582/1‑68 (MQ=255)

 cAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCa                                                                    >  1:12880357/1‑68 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAGGGGATCATCCAGt                                                                  >  1:22402140/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGt                                                                  >  1:25002608/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGt                                                                  >  1:31360507/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGt                                                                  >  1:33191593/1‑66 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGt                                                                  <  1:13339780/66‑1 (MQ=255)

     ttGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGt                                                                  <  1:5629138/66‑1 (MQ=255)

     tcgAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGt                                                                  >  1:11980018/3‑66 (MQ=255)

      tGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCt                                                               >  1:33959095/1‑68 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                            >  1:20981529/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                            >  1:19252696/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                            >  1:32259896/1‑67 (MQ=255)

          aCCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCtttt                                                            >  1:6506071/1‑67 (MQ=255)

           ccAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTATTTTTc                                                          >  1:7449306/1‑68 (MQ=255)

              aTCACGTCAAATTACCGGCGGTGGTGTACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCga                                                        >  1:4145464/1‑67 (MQ=255)

              aTCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCgaa                                                       <  1:14085604/68‑1 (MQ=255)

                     cAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACg                                                 <  1:10230815/67‑1 (MQ=255)

                     cAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACg                                                 <  1:15690758/67‑1 (MQ=255)

                      aaaTTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCa                                               <  1:5410581/68‑1 (MQ=255)

                      aaaTTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCa                                               <  1:32778217/68‑1 (MQ=255)

                       aaTTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCaa                                              >  1:6319120/1‑68 (MQ=255)

                        aTTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAg                                             <  1:1218305/68‑1 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCTTCCAGTTCTTTTTCGAAGAAACGCAAg                                             >  1:28773115/1‑67 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAg                                             >  1:949858/1‑67 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAg                                             >  1:24589664/1‑67 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGa                                            <  1:9102487/68‑1 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGa                                            <  1:20139298/68‑1 (MQ=255)

                         ttACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGa                                            <  1:5017937/68‑1 (MQ=255)

                             cggcggTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACgag                                        >  1:966599/1‑68 (MQ=255)

                             cggcggTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACgag                                        >  1:20905363/1‑68 (MQ=255)

                              ggcggTGGTGGACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACgaga                                       <  1:11788764/68‑1 (MQ=255)

                                   tggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATgg                                   <  1:17107200/67‑1 (MQ=255)

                                   tggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATgg                                   <  1:6570901/67‑1 (MQ=255)

                                   tggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATgg                                   <  1:22986741/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCTTCGAAGGGATAATCCCGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:20417752/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:12527859/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:10706384/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:3002785/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:23463242/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:15026277/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:8717619/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:5229103/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:24248666/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:28034723/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:19614163/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:31172330/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:27259954/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGc                                  <  1:21908321/67‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCt                                 <  1:2651523/68‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCt                                 <  1:2134913/68‑1 (MQ=255)

                                    ggtggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCt                                 <  1:11563665/68‑1 (MQ=255)

                                      tggACGGCTTTGCCAGCGAAGGGGTCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCtt                                <  1:4024293/67‑1 (MQ=255)

                                      tggACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCttt                               >  1:1472895/1‑68 (MQ=255)

                                      tggACGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCttt                               >  1:16379328/1‑68 (MQ=255)

                                       ggACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTa                              >  1:10947794/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:17590132/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:3240547/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:33560610/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:22836928/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:2325437/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:8143609/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:13590427/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTaa                             <  1:26758481/67‑1 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                            >  1:240225/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                            >  1:28175809/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                            >  1:20265903/1‑68 (MQ=255)

                                         aCGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                            >  1:26108342/1‑68 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                           <  1:16824747/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGATGAAACGCAAGACGAGAATGGCTTTAata                           <  1:29683149/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                           <  1:30579595/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                           <  1:29809617/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                           <  1:18225355/68‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                            <  1:24390864/67‑1 (MQ=255)

                                          cGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAat                            <  1:34269364/67‑1 (MQ=255)

                                           ggCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAATGCAAGACGAGAATGGCTTTAata                           >  1:31738122/1‑67 (MQ=255)

                                           ggCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAatat                          <  1:19044726/68‑1 (MQ=255)

                                            gCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAata                           >  1:8483220/1‑66 (MQ=255)

                                              tttGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCt                        <  1:19457069/67‑1 (MQ=255)

                                                   cAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTa                       >  1:29447045/1‑63 (MQ=255)

                                                       gAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATtct                 <  1:25501638/65‑1 (MQ=255)

                                                       gAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTcga              <  1:10091173/68‑1 (MQ=255)

                                                           ggATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaa          >  1:27624345/1‑68 (MQ=255)

                                                           ggATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaa          >  1:18527637/1‑68 (MQ=255)

                                                            gATCATCTAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:15270578/1‑68 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTcgacga           <  1:26935630/66‑1 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:29097744/1‑68 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:25720124/1‑68 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:6946325/1‑68 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:7166359/1‑68 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:23891458/1‑68 (MQ=255)

                                                            gATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:23754656/1‑68 (MQ=255)

                                                             atcatcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGaaa         >  1:11329381/1‑67 (MQ=255)

                                                              tcatcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGc       >  1:28535473/1‑68 (MQ=255)

                                                               catcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCa      <  1:4714859/68‑1 (MQ=255)

                                                               catcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCa      <  1:22599859/68‑1 (MQ=255)

                                                               catcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCa      <  1:3338920/68‑1 (MQ=255)

                                                                 tcCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGGaa     >  1:33793345/1‑67 (MQ=255)

GCAGGTTGAAACCAATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCG  >  CP009273/3986672‑3986806

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`