BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,595,993	T→A	6.5%	intergenic (‑11/+24)	leuV ← / ← leuP	tRNA‑Leu/tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,595,993	0	T	A	6.5%	822.8 / 4.6	289	intergenic (‑11/+24)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base T (121/140); new base A (4/18); total (131/158)
Fisher's exact test for biased strand distribution p-value = 1.28e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 320 total aligned reads displayed.

CCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACAC  >  CP009273/4595928‑4596060

    aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttt                                                                >  1:4455885/1‑68 (MQ=255)

    aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttt                                                                 <  1:33010509/67‑1 (MQ=255)

    aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATATGAAtttt                                                                >  1:28056860/1‑68 (MQ=14)

    aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAGCGGACtttg                                                                >  1:27712167/1‑67 (MQ=14)

    aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAGATTACtttt                                                                >  1:3559056/1‑68 (MQ=255)

     aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                               <  1:10676894/68‑1 (MQ=255)

     aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                               <  1:2953714/68‑1 (MQ=255)

     aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                               <  1:38204614/68‑1 (MQ=255)

      ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttttt                                                              >  1:18263522/1‑68 (MQ=255)

      ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttata                                                              >  1:16698371/1‑65 (MQ=255)

          acTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTAAATTTTTTTGat                                                          >  1:24972093/1‑68 (MQ=255)

             aaCACCTGAAGCTAGCGCTTAAACAAATTCCGACACCTTCGCACACTCGACTTACTTTTTTTGattta                                                       >  1:2290577/1‑65 (MQ=12)

             aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATc                                                       <  1:22494040/68‑1 (MQ=255)

             aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGGAAGCTTACTTTTTTTGATTTc                                                       >  1:11463228/1‑68 (MQ=17)

              acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                      <  1:17357507/68‑1 (MQ=255)

               cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                     <  1:23185862/68‑1 (MQ=255)

               cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                     <  1:13870507/68‑1 (MQ=255)

               cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                     <  1:39216639/68‑1 (MQ=255)

               cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                     <  1:10431175/68‑1 (MQ=255)

                acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTCATCTGACTTTTTTTGATATCGcg                                                    >  1:29084331/1‑67 (MQ=18)

                acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCAGAGGCAGATTACTTTTTTTGATTTCgac                                                    >  1:27076201/1‑66 (MQ=17)

                acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGcc                                                    >  1:25137817/1‑68 (MQ=255)

                 ccTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCCTCGGACTTTTTTTGATATCGca                                                    >  1:10261234/1‑66 (MQ=18)

                   ttaaGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:18698199/66‑1 (MQ=255)

                   tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:27344586/68‑1 (MQ=255)

                   tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:14812685/68‑1 (MQ=255)

                   tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:25483986/68‑1 (MQ=255)

                   tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:3292100/68‑1 (MQ=255)

                   tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:21306181/68‑1 (MQ=255)

                   tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:7464414/68‑1 (MQ=255)

                      aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGttt                                              >  1:26941315/1‑68 (MQ=255)

                      aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGtt                                               <  1:11182544/67‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGGCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:26548238/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:36648460/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:14589257/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:12463148/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:6334855/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:572151/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:3056545/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:7246671/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:17692189/68‑1 (MQ=255)

                              cgTCTACCAATTCCGCCACCTTCGCACAGTCATATTACTTTATATGATTTCGCCTCGGTTGGGGCGA‑g                                     >  1:23742122/1‑68 (MQ=21)

                               gTCTTCCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑g                                     <  1:5779716/67‑1 (MQ=255)

                                 cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑ggg                                   <  1:32084898/67‑1 (MQ=255)

                                 cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑ggg                                   <  1:15188215/67‑1 (MQ=255)

                                 aaaCCAATTCCGCCACCTTCGCACAGTCAACTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑ggg                                   <  1:37037308/65‑1 (MQ=255)

                                   aCCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:33372501/52‑1 (MQ=255)

                                      aaatCCGCCACCTTCTCACAGTCATCTTACTTTTTTTGATATCCCCTCCTTTGGTGCGA‑GGGGGGGGa                             <  1:3398543/65‑1 (MQ=38)

                                      aaatCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGa                             <  1:3862032/65‑1 (MQ=255)

                                      aaatCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCCTTTGGTGCGA‑GGGGGGGGa                             <  1:36022226/65‑1 (MQ=255)

                                      aaatCCGCCACCTTCGCACAGGCATCATACATTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGa                             <  1:25843852/65‑1 (MQ=38)

                                      aaTTCCGCCACCTTCGCACAGTGCTCTTAGTTATTTTGAGATCCCCTCGTTTGTTGCGA‑GGGGGGGGa                             >  1:9102877/1‑68 (MQ=25)

                                       aTTCCGCCACCTTCGCACAGGCTTATTTCTTTTTTTGATTTCGGAGCGGGTGGTGCGA‑gggggggg                              >  1:14245188/1‑66 (MQ=255)

                                         tCCGCCACCTTCGCACAGTCATCGTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACtt                          >  1:11921655/1‑68 (MQ=255)

                                          ccGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACtt                          >  1:3456592/1‑67 (MQ=255)

                                          ccGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTg                         >  1:22580258/1‑68 (MQ=255)

                                           cGCCACCTTCGCACAGTCAACTAACTTTTTTTGATATCCCCACCTTTGGTGCGA‑GGGGGGGGACTTGa                        <  1:20127157/68‑1 (MQ=25)

                                            gCCACCTACTCACAGTCATCTTACTTTTTTTGAAATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGaa                       <  1:37614445/68‑1 (MQ=37)

                                               aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                     >  1:8739899/1‑67 (MQ=255)

                                               aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                     >  1:9425404/1‑67 (MQ=255)

                                               aCCTTCCCACAGTCATCTAACATTTTTTGATATCCCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                    <  1:807508/68‑1 (MQ=25)

                                               aCCTACGCACACGCATCATACTTTTTTTGAAATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                    <  1:17477505/68‑1 (MQ=25)

                                               aCCATCCCACAGTCATCATACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                    <  1:2897763/68‑1 (MQ=37)

                                                cgttCGCACAGGCATCATACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcccc                   <  1:19263663/66‑1 (MQ=37)

                                                 cTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGGACTTGAAccc                    >  1:19772917/1‑67 (MQ=255)

                                                 cTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccac                   >  1:14909999/1‑65 (MQ=255)

                                                     caacacTCATCATACATTTTTTGAAATAACCTCATTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt              <  1:30997568/66‑1 (MQ=17)

                                                      cacaGTCATCATACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTc             <  1:20863626/68‑1 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGGCCTTGAACCCCCACGt              >  1:11706442/1‑67 (MQ=37)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:36406698/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:5138009/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:9622337/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:30893051/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGACTCGTTTGGAGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:20967365/1‑68 (MQ=25)

                                                        caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           >  1:10001148/1‑68 (MQ=255)

                                                        caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           >  1:13199106/1‑68 (MQ=255)

                                                        caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           >  1:15865178/1‑68 (MQ=255)

                                                         aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGt          >  1:33265732/1‑68 (MQ=255)

                                                          gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa         >  1:4890917/1‑68 (MQ=255)

                                                          gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACACCAACGTCCGTa         >  1:2432085/1‑68 (MQ=255)

                                                            caacTTACTTTTTTTGATATCCCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:6743899/61‑1 (MQ=255)

                                                            cATCTTACTTTTTTTGATTTCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:12973255/64‑1 (MQ=255)

                                                            cATCTTACTTTTTTTGATATCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:26316901/64‑1 (MQ=255)

                                                            cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa         <  1:24822242/66‑1 (MQ=255)

                                                            cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAg       >  1:37783835/1‑68 (MQ=255)

                                                            cATCTAACTTTTTTTGATATCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAg       <  1:12315358/68‑1 (MQ=255)

                                                            cATCTAACTTTTTTTGAAATCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAg       <  1:34401899/68‑1 (MQ=18)

                                                             aTCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:15709045/68‑1 (MQ=255)

                                                             aTCTTACTTTTTTTGAAATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:31426405/68‑1 (MQ=255)

                                                             aTCATACATTTTTTGATATCGCCTCCTTTGGTGCTA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:13281285/68‑1 (MQ=18)

                                                               cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:17145340/1‑68 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTTGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:30124047/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGCACCCCCACGTCCGTAAGAac    >  1:22366553/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                     >  1:20394818/1‑49 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:18118443/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:21899185/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:36172132/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:8580372/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:38755211/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:23610616/1‑66 (MQ=255)

CCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACAC  >  CP009273/4595928‑4596060

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: `‑`