BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,351,426	G→T	5.4%	Q44H (CAG→CAT)	ypaA →	uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,351,426	0	G	T	5.4%	3704.4 / 26.5	1065	Q44H (CAG→CAT)	ypaA	uncharacterized protein
Reads supporting (aligned to +/- strand): ref base G (487/506); new base T (69/2); total (557/508)
Fisher's exact test for biased strand distribution p-value = 5.40e-18
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 1082 total aligned reads displayed.

AAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGCCC  >  CP009273/2351359‑2351493

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:37499962/1‑68 (MQ=255)

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:35295450/1‑68 (MQ=255)

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:45059729/1‑68 (MQ=255)

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:30133307/1‑68 (MQ=255)

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:48232235/1‑68 (MQ=255)

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:21168703/1‑68 (MQ=255)

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:54504269/1‑68 (MQ=255)

  ggTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   >  1:17832911/1‑68 (MQ=255)

    attGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGt                                                                   <  1:29089002/65‑1 (MQ=255)

     atGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACCATGTGc                                                                 >  1:13459253/2‑67 (MQ=11)

         aTGAACAAGCCATTAAACTTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTcgcg                                                            <  1:37157594/68‑1 (MQ=255)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACAATGTGCTcgcg                                                            >  1:1288091/1‑68 (MQ=11)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACAAGGTGCTcgcg                                                            >  1:16098370/1‑68 (MQ=255)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAg                                                                     >  1:45662584/1‑59 (MQ=255)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTcgcg                                                            >  1:14436621/1‑68 (MQ=255)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTcgcg                                                            <  1:2861101/68‑1 (MQ=255)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTcgcg                                                            <  1:53670142/68‑1 (MQ=255)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTcgcg                                                            <  1:55038706/68‑1 (MQ=255)

         aTGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACAAGGTGCTcgcg                                                            >  1:25037338/1‑68 (MQ=255)

          tGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACAATGTGCTcgcg                                                            >  1:17175266/1‑67 (MQ=11)

          tGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACAATGTGCTcgcg                                                            >  1:44593327/1‑67 (MQ=11)

          tGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACAATGTGCTcgcg                                                            >  1:34076946/1‑67 (MQ=11)

          tGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGAACGTGACCATGTGCTcgcg                                                            >  1:25962791/1‑67 (MQ=11)

          tGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTcgcg                                                            >  1:2032716/1‑67 (MQ=255)

          tGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTcgcg                                                            >  1:50283832/1‑67 (MQ=255)

             aCAAGCCATTAAAATTGCTTTGCGCATGCTGGATCAGGGCTTTGATCGTGACAAGGTGCTcgcgcca                                                         >  1:27799491/1‑64 (MQ=17)

             aCAAGCCATTAAAATTGCTTTGCGCATGCTGGACCAGGGCTTTGATCGTGACCAGGTGCTCGCGGcc                                                         >  1:33586773/1‑67 (MQ=255)

             aCAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGcc                                                         <  1:47764340/67‑1 (MQ=255)

             aCAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGcc                                                         >  1:8159938/1‑67 (MQ=255)

             aCAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGcc                                                         >  1:25523552/1‑67 (MQ=255)

             aCAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGcc                                                         >  1:55916207/1‑67 (MQ=255)

              cAAGCCATTAAAATTGCTTCGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCAc                                                       <  1:54069414/68‑1 (MQ=255)

                  ccATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCa                                                    >  1:3887605/1‑67 (MQ=255)

                      tAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTaa                                               <  1:7227858/68‑1 (MQ=255)

                      tAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTaa                                               <  1:38454797/68‑1 (MQ=255)

                       aaaaTTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAg                                              <  1:10335693/68‑1 (MQ=255)

                         aaTTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCg                                            >  1:33078034/1‑68 (MQ=255)

                         aaTTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCg                                            >  1:41128593/1‑68 (MQ=255)

                           ttGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGaa                                          <  1:18292425/68‑1 (MQ=255)

                             gCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACAATGTGCTCGCGGCCACCCACCTAAGCGATGc                                        >  1:52662193/1‑68 (MQ=18)

                               tttGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGcc                                       <  1:47096638/67‑1 (MQ=255)

                               tttGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCg                                      >  1:45974872/1‑68 (MQ=255)

                               tttGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCg                                      <  1:8660594/68‑1 (MQ=255)

                                      aTGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTgg                                <  1:16473071/67‑1 (MQ=255)

                                         cTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGc                            >  1:43913355/1‑68 (MQ=255)

                                         cTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGc                            >  1:57119278/1‑68 (MQ=255)

                                          tGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCg                           <  1:32071499/68‑1 (MQ=255)

                                           ggAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGa                          <  1:14993660/68‑1 (MQ=255)

                                              aCAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCTAAGCCGATCTGGCAGCGAATa                       >  1:39352050/1‑68 (MQ=255)

                                              aCAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCTAAGCCGATCTGGCACCGAATa                       >  1:2064183/1‑68 (MQ=255)

                                              aCAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCCGCGAATa                       >  1:22170850/1‑68 (MQ=255)

                                              aCAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATa                       >  1:36799703/1‑68 (MQ=255)

                                              aCAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATa                       >  1:2433505/1‑68 (MQ=255)

                                                   gCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAAcc                    >  1:34852936/1‑66 (MQ=255)

                                                   gCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAAcc                    <  1:26521935/66‑1 (MQ=255)

                                                   gCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAAcc                    <  1:19295367/66‑1 (MQ=255)

                                                   gCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAAcc                    <  1:51311818/66‑1 (MQ=255)

                                                   gCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAAc                     <  1:11760479/65‑1 (MQ=255)

                                                     tttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACt                 <  1:5552885/67‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:53096547/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:10031946/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:48586974/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:23834225/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:46490270/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:27196943/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:52128005/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:21694805/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:31442348/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:19913617/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:19006458/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:40702340/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:12503693/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:57649226/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:681148/68‑1 (MQ=255)

                                                      ttGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTaa               <  1:9344978/68‑1 (MQ=255)

                                                        gATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAAtt             >  1:49661649/1‑68 (MQ=255)

                                                        gATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAAtt             >  1:36369556/1‑68 (MQ=255)

                                                        gATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAAtt             >  1:32693626/1‑68 (MQ=255)

                                                        gATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAAtt             >  1:43377557/1‑68 (MQ=255)

                                                         aTCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTa            >  1:5081895/1‑68 (MQ=255)

                                                          tCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTa            <  1:5868676/67‑1 (MQ=255)

                                                          tCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTa            >  1:42076376/1‑67 (MQ=255)

                                                           cGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAac          <  1:2333650/68‑1 (MQ=255)

                                                           cGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAac          <  1:42500418/68‑1 (MQ=255)

                                                           cGTGACCAGGTGCTCGCGGCAACCCAGCTAAGCGTAGCCGATCTGGCAGCGAATAACCACTAATTAac          <  1:14093421/68‑1 (MQ=255)

                                                               aCCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAg      >  1:6518431/1‑68 (MQ=255)

                                                               aCCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAg      >  1:7883715/1‑68 (MQ=255)

                                                                ccAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAg      >  1:30508514/1‑67 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGTATAACCACTAATTAACACAGGc    <  1:1099080/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACTACTAATTAACACAGGc    <  1:36033943/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    <  1:42895101/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    <  1:1572075/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    <  1:30929237/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    <  1:39973399/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    <  1:12201234/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    <  1:28242238/68‑1 (MQ=255)

                                                                 cAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    <  1:37982167/68‑1 (MQ=255)

                                                                  aGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGc    >  1:4911738/1‑67 (MQ=255)

                                                                   ggTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGccc  >  1:56460198/1‑68 (MQ=255)

                                                                   ggTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGccc  >  1:40437716/1‑68 (MQ=255)

AAGGTTTGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGCCC  >  CP009273/2351359‑2351493

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: `‑`