BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,595,993	T→A	8.9%	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	8.9%	619.4 / 9.8	234	intergenic (‑11/+24)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base T (99/110); new base A (2/21); total (103/131)
Fisher's exact test for biased strand distribution p-value = 2.51e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 288 total aligned reads displayed.

TCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACT  >  CP009273/4595927‑4596061

 ccGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTAc                                                                     <  1:21423166/68‑1 (MQ=255)

      aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                                <  1:246964/68‑1 (MQ=255)

      aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                                <  1:33439294/68‑1 (MQ=255)

      aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                                >  1:13736456/1‑68 (MQ=255)

       ggACACTAACACCTGAAGCTAGCGCTTCTACCAATTACGCCGCCATCGCACAGTCAGCGTAGttttta                                                               >  1:8700297/1‑67 (MQ=14)

       ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGACAAATTTCtttttt                                                               >  1:10003148/1‑68 (MQ=14)

           acTAACACCTGAAGCTACCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGat                                                           <  1:9208343/68‑1 (MQ=255)

               acacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                       <  1:28428275/68‑1 (MQ=255)

                cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                      <  1:12418918/68‑1 (MQ=255)

                cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                      <  1:8844837/68‑1 (MQ=255)

                cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                      <  1:3554219/68‑1 (MQ=255)

                 acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                       >  1:37851710/1‑66 (MQ=255)

                    tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                  <  1:22926004/68‑1 (MQ=255)

                    tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                  <  1:21655349/68‑1 (MQ=255)

                    tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                  <  1:29370195/68‑1 (MQ=255)

                    tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                  <  1:20264984/68‑1 (MQ=255)

                    tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                  <  1:4921552/68‑1 (MQ=255)

                    tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                  <  1:18546443/68‑1 (MQ=255)

                    tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                  <  1:32154823/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:25031411/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:30287236/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:5006903/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:19793005/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:36758646/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:37619374/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:11362188/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:6290495/68‑1 (MQ=255)

                          tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                            <  1:12554358/68‑1 (MQ=255)

                           aGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTg                                           <  1:755262/68‑1 (MQ=255)

                              gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTGACTTTTTTTGATATCGACTCGTTTGGTGCGa                                        >  1:38824929/1‑68 (MQ=255)

                                gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑g                                      <  1:25400856/67‑1 (MQ=255)

                                  cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑ggg                                    <  1:18302810/67‑1 (MQ=255)

                                  cTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑ggg                                    <  1:3091264/67‑1 (MQ=255)

                                  cTACCAATTCCGCCACCATCGCACATTCATCTAACTTTTTTTGATATCCCCTCGTTTGGTGCGA‑gggg                                   <  1:29817952/68‑1 (MQ=38)

                                  atACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑ggg                                    <  1:2696736/66‑1 (MQ=255)

                                    aCCAATTCCGCCACCTTCGCACAGTCATCATACTATATTTGATCTCGCCTCGTTTGGTGCGA‑gggggg                                 <  1:16729944/68‑1 (MQ=37)

                                       aaatCCGCCACCTTCGCACAGTCATCAAACTATATATGATATCCCCTCGTTTGGTGCGA‑GGGGGGGGa                              <  1:6590626/65‑1 (MQ=25)

                                        aatCCGCCACCAACGCACAGGCATCTTACATTTTTTGAAATCGCCTCTATTGGTGCGA‑GGGGGGGGAc                             <  1:22463922/66‑1 (MQ=25)

                                          tCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCGCGGTTGGGGCGA‑GGGGGGGGACtt                           >  1:3109140/1‑68 (MQ=255)

                                          tCCGCCACCTTCCCACAGTCATCTTACTTTTTTTGATATCCCCTCGTTTGGTGCGA‑GGGGGGGGACtt                           <  1:12852673/68‑1 (MQ=39)

                                            cGCCACCTTCGCACAGTCATCTTACTTTTTTTGATTTAGCCTCGATTGGTGCGA‑GGGGGGGGACTTGa                         <  1:38555138/68‑1 (MQ=38)

                                            cGCCACCAACGAACACTCATCATACTTTTTTTGAAATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGa                         <  1:37333509/68‑1 (MQ=18)

                                               cACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAc                       <  1:32468720/67‑1 (MQ=255)

                                                aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                      >  1:12220169/1‑67 (MQ=255)

                                                aCCTTCCCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                     <  1:3448414/68‑1 (MQ=255)

                                                aCCTACGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                     <  1:28079329/68‑1 (MQ=255)

                                                aCCTACGCACACTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                     <  1:7185372/68‑1 (MQ=255)

                                                aCCATCGCACAGTCATCTAACATTTTTTGATATCCCCGCGTTTGGGGCGACGGGGGGGGACTTGAAcc                      <  1:13003407/68‑1 (MQ=25)

                                                     ccaacaGTCATCTAACTTTTTTTGATATCGCCTTTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg                <  1:17884902/65‑1 (MQ=21)

                                                      gCACAGTCAGCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt               <  1:8959648/68‑1 (MQ=255)

                                                       cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt               >  1:18184700/1‑67 (MQ=255)

                                                       cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt               >  1:14310177/1‑67 (MQ=255)

                                                       aacaGTCATCAAACATTTATTGAATTCCCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTc              <  1:2219931/67‑1 (MQ=17)

                                                        acacTCAACTAACTTTTTTTGAAATCGCCTAGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             <  1:18731123/68‑1 (MQ=18)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTTCGA‑GGGGGGGGACTTGAACCCCCACGAcc             >  1:8236467/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGACCCCCCACGTcc             >  1:20348584/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:17343541/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:10348070/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:37144758/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:10613837/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:10988147/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:13461706/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:14720123/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:4530378/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:2768540/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:17944768/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:31714614/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:31436118/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:18831587/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:22001982/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:5848380/1‑68 (MQ=255)

                                                        acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc             >  1:27396613/1‑68 (MQ=255)

                                                         caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg            >  1:15020230/1‑68 (MQ=255)

                                                         caGTCATCTTAATTTTTTTGATTTCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg            <  1:12775653/68‑1 (MQ=18)

                                                           gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa          >  1:5988297/1‑68 (MQ=255)

                                                            tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTaa         >  1:36277313/1‑68 (MQ=255)

                                                             catcatACTTTTTTTGATCTCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg            <  1:15901980/64‑1 (MQ=18)

                                                             cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTaa         >  1:9547567/1‑67 (MQ=255)

                                                             cATCTAACTTTTTTTGAACTCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa          <  1:24356932/66‑1 (MQ=18)

                                                             cATCTAACTTTATTTGATATACCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg            <  1:35309692/64‑1 (MQ=17)

                                                                cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGCac     >  1:26168018/1‑68 (MQ=255)

                                                                cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:13992680/1‑68 (MQ=255)

                                                                 ttACTTTTTTTGAATTCTCGTCTCTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca    <  1:6660003/68‑1 (MQ=14)

                                                                 ttACTTTTTTTGAAATCCCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca    <  1:26443366/68‑1 (MQ=18)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGCac     >  1:31257035/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:4032486/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:32699527/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:14435558/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:1543809/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:16099185/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:16467580/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:8462147/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:17088623/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:21050425/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:33043041/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:36311379/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:27597202/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:30559304/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac     >  1:30825770/1‑66 (MQ=255)

                                                                  tACTTTTTTTGATATCCCCTCCTTTGGTTCGA‑‑GTGGGGGACTTGAACGACCACGTCCGTAAGAACACt  >  1:35135795/1‑68 (MQ=18)

TCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACT  >  CP009273/4595927‑4596061

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: `‑`