BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	1,241,461	A→G	10.5%	W458R (TGG→CGG)	treA ←	periplasmic trehalase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	1,241,461	0	A	G	10.5%	2105.2 / 165.8	678	W458R (TGG→CGG)	treA	periplasmic trehalase
Reads supporting (aligned to +/- strand): ref base A (237/365); new base G (27/44); total (267/411)
Fisher's exact test for biased strand distribution p-value = 8.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01

Only 100 of 700 total aligned reads displayed.

AGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGG  >  CP009273/1241395‑1241528

aGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCa                                                                     <  1:16423023/67‑1 (MQ=255)

aGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCa                                                                     <  1:16211663/67‑1 (MQ=255)

aGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCa                                                                     <  1:7422238/67‑1 (MQ=255)

aGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCa                                                                     <  1:2016053/67‑1 (MQ=255)

aGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCAc                                                                    <  1:15776332/68‑1 (MQ=255)

 ttGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:19246866/67‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCt                                                                   <  1:11509080/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:21085664/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:17182034/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:31107254/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:30276628/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:35919818/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:21758935/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:4294834/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:28935181/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:2354525/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:2621220/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:28063757/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:32410370/66‑1 (MQ=255)

   gCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACt                                                                   <  1:15418722/66‑1 (MQ=255)

    ccAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTa                                                                >  1:13761753/1‑68 (MQ=255)

        cTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGACCCCACAGTAACg                                                             >  1:16931784/1‑68 (MQ=255)

        cTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACgg                                                            >  1:23096299/1‑68 (MQ=255)

         tAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTTTAATCCTTCTGTCGCGA‑CCCACTGTAACGGt                                                           <  1:34233988/68‑1 (MQ=255)

         tAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGt                                                           <  1:16740037/68‑1 (MQ=255)

           aTGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGc                                                         <  1:22441835/68‑1 (MQ=255)

             gTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGccc                                                       >  1:3185719/1‑68 (MQ=255)

             gTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGccc                                                       >  1:25116035/1‑68 (MQ=255)

              tCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCa                                                      >  1:8419949/1‑68 (MQ=255)

              tCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGcccc                                                      >  1:22571776/1‑67 (MQ=255)

              tCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCa                                                      >  1:13421353/1‑68 (MQ=255)

              tCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCa                                                      >  1:26014148/1‑68 (MQ=255)

              tCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGAGCCCa                                                      >  1:706158/1‑68 (MQ=255)

               ccATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCa                                                      >  1:6366259/1‑67 (MQ=255)

               ccATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCa                                                      >  1:23706733/1‑67 (MQ=255)

               ccATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCa                                                      >  1:24076639/1‑67 (MQ=255)

                cATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGc                                                    <  1:37002492/68‑1 (MQ=255)

                cATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGc                                                    <  1:25355664/68‑1 (MQ=255)

                 aTCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGcc                                                   >  1:4717921/1‑68 (MQ=255)

                  tCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCa                                                  <  1:36656162/68‑1 (MQ=255)

                  tCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCa                                                  <  1:12365735/68‑1 (MQ=255)

                   cGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCAt                                                 <  1:5639421/68‑1 (MQ=255)

                    gCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGCCAtt                                                >  1:3559185/1‑68 (MQ=255)

                    gCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCAtt                                                >  1:32153208/1‑68 (MQ=255)

                    gCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCAtt                                                >  1:19781860/1‑68 (MQ=255)

                    gCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCAtt                                                >  1:3649685/1‑68 (MQ=255)

                         ctctTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGgc                                            >  1:6814506/1‑67 (MQ=255)

                          tctTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGgcgc                                          >  1:2679538/1‑68 (MQ=255)

                            tttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGCCATTTGGCGCa                                         >  1:18071796/1‑67 (MQ=255)

                            tttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCAt                                        <  1:6037615/68‑1 (MQ=255)

                            tttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCAt                                        <  1:3317923/68‑1 (MQ=255)

                             ttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGCCATTTGGCGCATc                                       <  1:22135033/68‑1 (MQ=255)

                             ttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGCCATTTGGCGCATc                                       <  1:5295873/68‑1 (MQ=255)

                             ttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATc                                       <  1:26914152/68‑1 (MQ=255)

                             ttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATc                                       <  1:35201580/68‑1 (MQ=255)

                             ttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATc                                       <  1:29541902/68‑1 (MQ=255)

                             ttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATc                                       <  1:18500784/68‑1 (MQ=255)

                             ttttGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATc                                       <  1:10308995/68‑1 (MQ=255)

                                tGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCa                                    >  1:29994827/1‑68 (MQ=255)

                                  cccGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGCCATTTGGCGCATCCCAtt                                  >  1:24734822/1‑68 (MQ=255)

                                  cccGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCAtt                                  >  1:7903093/1‑68 (MQ=255)

                                  cccGTAGTTTTGTAATCCTCCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGCCATTTGGCGCATCCCAtt                                  >  1:32862458/1‑68 (MQ=255)

                                   ccGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCAtt                                  <  1:3970707/67‑1 (MQ=255)

                                    cGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCGCTGTAACGGTGCCCAGCCATTTGGCGCATCCCAttgt                                <  1:17681592/68‑1 (MQ=255)

                                    cGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCAttgt                                <  1:18631512/68‑1 (MQ=255)

                                       aGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGGGCCCAGCCATTTGGCGCATCCCATTGTTGc                             <  1:9674918/68‑1 (MQ=255)

                                           ttGTAATCCTTCTGTCGCGC‑CCCACTGTAACGGGGCCCAGCCATTTGGCGCATCCCATTGTTGCCCAc                         <  1:33303362/68‑1 (MQ=255)

                                            tGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACt                        >  1:7229397/1‑68 (MQ=255)

                                            tGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACt                        <  1:2782302/68‑1 (MQ=255)

                                             gTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACtt                       >  1:32586668/1‑68 (MQ=255)

                                             gTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACtt                       >  1:10009385/1‑68 (MQ=255)

                                             gTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACtt                       >  1:10775456/1‑68 (MQ=255)

                                             gTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACtt                       >  1:12690010/1‑68 (MQ=255)

                                             gTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACtt                       >  1:20658824/1‑68 (MQ=255)

                                                  ccTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCa                   >  1:30922896/1‑67 (MQ=255)

                                                  ccTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCa                   >  1:33443701/1‑67 (MQ=255)

                                                  ccTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCa                   >  1:29756208/1‑67 (MQ=255)

                                                  ccTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCa                   >  1:25743314/1‑67 (MQ=255)

                                                   cTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCAcc                 <  1:3146814/68‑1 (MQ=255)

                                                   cTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCAcc                 <  1:33840188/68‑1 (MQ=255)

                                                     tCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGa               <  1:28454868/68‑1 (MQ=255)

                                                        gTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgt            <  1:2652451/68‑1 (MQ=255)

                                                        gTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgt            >  1:34573776/1‑68 (MQ=255)

                                                          cgcgA‑CCCGCTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgggg          >  1:12960557/1‑68 (MQ=255)

                                                          cgcgA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCGTCCCATTGTTGCCCACTTTTCACCGACgtgg          >  1:34728355/1‑68 (MQ=255)

                                                          cgcgA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgtgg          >  1:8696187/1‑68 (MQ=255)

                                                          cgcgA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgtgg          <  1:11888292/68‑1 (MQ=255)

                                                          cgcgA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgtgg          >  1:757987/1‑68 (MQ=255)

                                                          cgcgA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgtgg          >  1:28586523/1‑68 (MQ=255)

                                                          cgcgA‑CACACTGTAACGGTGCCAAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACttgg          >  1:21276478/1‑68 (MQ=255)

                                                           gcgA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACgtgtg         <  1:9122494/68‑3 (MQ=255)

                                                             gA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGgtgt       <  1:27234004/68‑1 (MQ=255)

                                                             gA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGgtgt       <  1:35324982/68‑1 (MQ=255)

                                                             gA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGgtgt       <  1:20890691/68‑1 (MQ=255)

                                                             gA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGgtgt       <  1:2198453/68‑1 (MQ=255)

                                                                cccGCTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTc     >  1:36181323/1‑68 (MQ=255)

                                                                cccACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTc     >  1:14114570/1‑68 (MQ=255)

                                                                cccACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTc     >  1:14599693/1‑68 (MQ=255)

                                                                cccACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTGTTCACGGACGTGGTGTTc     >  1:22857954/1‑68 (MQ=255)

                                                                   aCTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAgg  <  1:15008411/68‑1 (MQ=255)

AGTGCCAGCTAATGTCCATCGCCACCTCTTTTTGCCCGTAGTTTTGTAATCCTTCTGTCGCGA‑CCCACTGTAACGGTGCCCAGCCATTTGGCGCATCCCATTGTTGCCCACTTTTCACCGACGTGGTGTTCAGG  >  CP009273/1241395‑1241528

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: `‑`