BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,511,629	A→T	5.4%	intergenic (‑34/+6)	alaX ← / ← alaW	tRNA‑Ala/tRNA‑Ala

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,511,629	0	A	T	5.4%	1644.1 / 9.2	555	intergenic (‑34/+6)	alaX/alaW	tRNA‑Ala/tRNA‑Ala
Reads supporting (aligned to +/- strand): ref base A (306/209); new base T (15/25); total (321/234)
Fisher's exact test for biased strand distribution p-value = 7.84e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 570 total aligned reads displayed.

CATGCAAGCGCTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCTCTCCCAGC  >  CP009273/2511562‑2511696

    cAAGCGCTCTCCCAGCTGAGCTATAGCCCCGCGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAAt                                                                 >  1:3002995/1‑68 (MQ=255)

     aaGCGCTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAAtt                                                                >  1:29737118/1‑68 (MQ=255)

     aaGCGCTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAAt                                                                 <  1:6495169/67‑1 (MQ=255)

     aaGCGCTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAAt                                                                 <  1:2637367/67‑1 (MQ=255)

     aaGCGCTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAAt                                                                 <  1:38767721/67‑1 (MQ=255)

        cgcTCTCCCAGCTGAGCTATAGCCCCATGAGGGTTTTAATTTCCAAGTTTGCTGGGTGAAAAAtttta                                                             >  1:28601915/1‑66 (MQ=12)

        cgcTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCTATATTtgg                                                             >  1:31653292/1‑68 (MQ=255)

        cgcTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCTAAATTtgg                                                             >  1:10982830/1‑68 (MQ=255)

         gcTCTCCCAGCTGAGCTATAGCCCCGAGAGGGTTATACGTACCAAGTTTCCGGGGTGAAAAATTtggt                                                            >  1:25030766/1‑68 (MQ=16)

         gcTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTtggt                                                            >  1:23879912/1‑68 (MQ=255)

         gcTCTCCCAGCTGAGCTATAGCCCCACGAGGGATTTAGTTACCAAGTTTGCTGGGGGCAAAATTtgtt                                                            >  1:22612227/1‑66 (MQ=21)

            ctcCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGa                                                         <  1:36427820/68‑1 (MQ=255)

            ctcCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGa                                                         <  1:3589168/68‑1 (MQ=255)

            ctcCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGa                                                         <  1:20848066/68‑1 (MQ=255)

             tcCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAg                                                        <  1:33234424/68‑1 (MQ=255)

             tcCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAg                                                        <  1:28929312/68‑1 (MQ=255)

             tcCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAg                                                        <  1:10422945/68‑1 (MQ=255)

                 aGCTGAGCTATAGCCCCGACAAGAAATTACGTACCAGGTTTCGGGCGTCAAAAATTTGGTTGAGCTaa                                                    >  1:15992253/1‑68 (MQ=255)

                 aGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTCCAAAATTTGGTGGAGCTaa                                                    >  1:31398419/1‑68 (MQ=255)

                 aGCTGAGCTATAGCCCCAAGAAGCGTTTACGTACCAATTTTGCTGCGTGAAAAATTTGGTGGAGCTaa                                                    >  1:30740059/1‑68 (MQ=255)

                   cTGAGCTATAGCCCCGCGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGc                                                  >  1:25666786/1‑68 (MQ=255)

                   cTGAGCTATAGCCCCCCGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGc                                                  >  1:28274043/1‑68 (MQ=255)

                   cTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGc                                                  >  1:33779607/1‑68 (MQ=255)

                   cTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGc                                                  >  1:12820237/1‑68 (MQ=255)

                   cTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGc                                                  >  1:27658576/1‑68 (MQ=255)

                   cTGAGCTATAGCCCCACGAGGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTACGc                                                  >  1:26719932/1‑68 (MQ=255)

                   cTGAGCTATAGCCCCACCATGCGTTTACGTACCAAGTTTGCTGGGTGCTAAATTTGGTGGAGCAAAGc                                                  >  1:21307186/1‑68 (MQ=255)

                    tgcgCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTaa                                                    <  1:28818271/62‑1 (MQ=255)

                    tGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTaa                                                    <  1:33542397/65‑1 (MQ=255)

                    tGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGGGGAGCTaa                                                    <  1:27409246/65‑1 (MQ=255)

                     gAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCgg                                                >  1:34211432/1‑68 (MQ=255)

                     gAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCgg                                                >  1:30641354/1‑68 (MQ=255)

                       gCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCggg                                               <  1:9649002/67‑1 (MQ=255)

                       gCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGa                                              >  1:18879191/1‑68 (MQ=255)

                       gCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGa                                              >  1:4241546/1‑68 (MQ=255)

                       gCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGa                                              >  1:7062634/1‑68 (MQ=255)

                         tataGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATc                                            >  1:10769559/1‑68 (MQ=255)

                            aGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGa                                          >  1:9244477/1‑67 (MQ=255)

                            aGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGa                                          >  1:6328164/1‑67 (MQ=255)

                             gCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCTAAATTTGGTGGAGCTAAGCGGGATCGaa                                         >  1:19857137/1‑67 (MQ=255)

                             gCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGaa                                         >  1:29332144/1‑67 (MQ=255)

                              ccccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:11328086/1‑68 (MQ=255)

                              ccccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:30444692/1‑68 (MQ=255)

                              ccccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:16548259/1‑68 (MQ=255)

                              ccccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:31323982/1‑68 (MQ=255)

                              ccccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:34868231/1‑68 (MQ=255)

                              ccccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:7840884/1‑68 (MQ=255)

                              ccccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:32214553/1‑68 (MQ=255)

                               cccACGATTCCTTTACGCACCAAGCTTGCTGGGTGCTAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       <  1:33096021/67‑1 (MQ=21)

                               cccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:10065720/1‑67 (MQ=255)

                               cccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       <  1:26527607/67‑1 (MQ=255)

                               cccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:18541215/1‑67 (MQ=255)

                               cccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:5146036/1‑67 (MQ=255)

                               cccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:8181531/1‑67 (MQ=255)

                               cccACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAAcc                                       >  1:3843658/1‑67 (MQ=255)

                                 cACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGC‑GGATCGAACCGCTg                                   >  1:670449/1‑68 (MQ=255)

                                  aCGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTg                                   >  1:33011425/1‑68 (MQ=255)

                                  aCGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTg                                   >  1:5837633/1‑68 (MQ=255)

                                   cGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:11497946/68‑1 (MQ=255)

                                   cGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:12037202/68‑1 (MQ=255)

                                   cGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:23179070/68‑1 (MQ=255)

                                   cGATGCGTTTACCTACCAAGCTTGGTGGGTGGAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:25372659/68‑1 (MQ=21)

                                   cGATGCGTATACGCACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:29189373/68‑1 (MQ=255)

                                   cGATGCGGTTACGGACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:19496349/68‑1 (MQ=255)

                                   cGATGCGATTACGAACCATGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:24470129/68‑1 (MQ=21)

                                   cGATGCGAATACGTACCAAGCTGCCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:26046381/68‑1 (MQ=18)

                                    gATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  >  1:16730375/1‑67 (MQ=255)

                                    gATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  >  1:31944145/1‑67 (MQ=255)

                                     ctGCGATTACGTACCAAGGATGCTGGGTGGTAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGa                                  <  1:15294759/65‑1 (MQ=17)

                                      tGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGAcc                                <  1:17887770/67‑1 (MQ=255)

                                      tGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGAcc                                >  1:13085701/1‑67 (MQ=255)

                                      tGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGAcc                                <  1:17249349/67‑1 (MQ=255)

                                      tGCGTTTACGTACCAAGTTTGCTGGGGGCTAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGAcc                                <  1:27891130/67‑1 (MQ=255)

                                      tGCGATAACGCACCAAGCTTGCTGGGTTCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGAcc                                <  1:26985235/67‑1 (MQ=17)

                                        acattACGTCCCAAGCTTGCTGGGTTGTAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACctct                             <  1:20266581/65‑1 (MQ=14)

                                         tattACGTACCAAGTTTCCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACctct                             <  1:34638161/65‑1 (MQ=255)

                                           ttACGGACCAAGCTTGGTGGGTGGTAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACctct                             <  1:3664981/65‑1 (MQ=14)

                                             aCGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGcat                        <  1:174617/68‑1 (MQ=255)

                                              cGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGcat                        >  1:34997915/1‑67 (MQ=255)

                                              cGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGcat                        >  1:21745360/1‑67 (MQ=255)

                                              cGTACCAAGCTTGCTGGGTTCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGcatg                       <  1:15035154/68‑1 (MQ=255)

                                               gTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGcatg                       >  1:18001191/1‑67 (MQ=255)

                                                 cccAAGTTTGCTGGGTTCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGcatgcc                     <  1:14473370/66‑1 (MQ=255)

                                                 aCCAAGTTTGCTGGGTTCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGcatgcc                     <  1:36590325/67‑1 (MQ=255)

                                                     aGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCa                >  1:13621746/1‑68 (MQ=255)

                                                        ttGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAgc             <  1:24159753/68‑1 (MQ=255)

                                                            tGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAgcgc           >  1:11866076/1‑66 (MQ=255)

                                                            tGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGctc         <  1:5601483/68‑1 (MQ=255)

                                                            tGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGctc         <  1:22419159/68‑1 (MQ=255)

                                                            tGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGctc         <  1:737379/68‑1 (MQ=255)

                                                            tGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGct          <  1:8663155/67‑1 (MQ=255)

                                                            tGGGTGCAAAATTTGGTGGAGCTAAGCGAGATCGAACCGCTGACCTCTTGCATGCCATGCAAgcgc           >  1:37730750/1‑66 (MQ=255)

                                                            tGGGTGCAAAATTTGGCGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGctc         <  1:3964339/68‑1 (MQ=255)

                                                             gggTGCTAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGctct        <  1:37264554/68‑1 (MQ=255)

                                                               gTGGAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCtctc       <  1:23432054/67‑1 (MQ=18)

                                                               gTGCTAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCtctc       <  1:4549567/67‑1 (MQ=18)

                                                               gTGCTAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCtctc       <  1:32560341/67‑1 (MQ=18)

                                                                 ggaaaaTTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCTCTCCCa    <  1:37897857/66‑1 (MQ=14)

                                                                  cAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCTCTCCCa    <  1:12347289/67‑1 (MQ=33)

                                                                   aaaaTTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCTCTCCCAGc  <  1:1924957/68‑1 (MQ=31)

CATGCAAGCGCTCTCCCAGCTGAGCTATAGCCCCACGATGCGTTTACGTACCAAGTTTGCTGGGTGCAAAATTTGGTGGAGCTAAGCGGGATCGAACCGCTGACCTCTTGCATGCCATGCAAGCGCTCTCCCAGC  >  CP009273/2511562‑2511696

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`