BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,595,993	T→A	12.2%	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	12.2%	604.5 / 15.8	228	intergenic (‑11/+24)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base T (99/97); new base A (3/27); total (104/124)
Fisher's exact test for biased strand distribution p-value = 1.82e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 262 total aligned reads displayed.

CCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACAC  >  CP009273/4595928‑4596060

ccGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCtt                                                                      >  1:24248712/1‑66 (MQ=255)

ccGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAGCtt                                                                      >  1:3193325/1‑66 (MQ=255)

 cGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACt                                                                   <  1:25632252/68‑1 (MQ=255)

    aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttt                                                                >  1:17156062/1‑68 (MQ=255)

    aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttt                                                                <  1:1587044/68‑1 (MQ=255)

     aGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACttttt                                                               <  1:10302513/68‑1 (MQ=255)

      ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttttt                                                              >  1:22869347/1‑68 (MQ=255)

      ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATATTTCtttttt                                                              >  1:18815033/1‑68 (MQ=255)

      ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATATAACtttaaa                                                              >  1:4254543/1‑65 (MQ=14)

      ggACACTAACACCTGAAGCTACCCCGACTACCAATTCCGCCACATTCGAACAGTGAGCTTACttttat                                                              >  1:22423151/1‑66 (MQ=14)

         cacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGa                                                           <  1:18238852/68‑1 (MQ=255)

          acTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGat                                                          <  1:5340942/68‑1 (MQ=255)

             aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATTTc                                                       >  1:21742565/1‑68 (MQ=255)

             aaCACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCAAATTACTTATTATGatatg                                                       >  1:27402502/1‑67 (MQ=17)

               cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                     <  1:28932045/68‑1 (MQ=255)

                acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                      >  1:7795640/1‑66 (MQ=255)

                acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTAATTTTTTTGATATCGcc                                                    >  1:29611069/1‑68 (MQ=255)

                acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGGCAGCTTACTTTTTTTGATATCGcc                                                    >  1:3975305/1‑68 (MQ=255)

                   tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                 <  1:917492/68‑1 (MQ=255)

                    gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGt                                                <  1:34725341/68‑1 (MQ=255)

                        cTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                            >  1:21247676/1‑68 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTTGTTTGGt                                           <  1:23252236/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:27197937/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:10705759/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:3082915/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:30754235/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:32028541/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:7285818/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:5906519/68‑1 (MQ=255)

                         tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                           <  1:11343946/68‑1 (MQ=255)

                             tagTCTACCAATTCCGCCACCTTCGCTCAGTCATCTTACTTTTTTTGATATCTCCTCGTTTGGTGCGa                                       <  1:20516575/66‑1 (MQ=37)

                             gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGa                                       >  1:378710/1‑68 (MQ=255)

                             gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGa                                       <  1:15465540/68‑1 (MQ=255)

                              cgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑g                                     >  1:3500219/1‑68 (MQ=255)

                               gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑g                                     <  1:23681322/67‑1 (MQ=255)

                                      aaTTCCGCCACCTACGCACAGTCATCATACTATTATTGATATCCCCTCGTTTGGTGCGA‑GGGGGGGGa                             <  1:26283955/68‑1 (MQ=37)

                                       aatCCGCCACCATCCCACAGTCATCATACATTTTTTGATATCGCCTCCTTTGGTGCGA‑GGGGGGGGAc                            <  1:3224246/66‑1 (MQ=37)

                                       aTTCCGCGATCTTCCCTCATTCATCTTACTTTATTTGATTTCTCCTCTATTGGTGCGA‑GGGGGGGGAc                            <  1:4151765/68‑1 (MQ=16)

                                       aTTCCGCCACCATACCACATTCATCAAACTTTTATTGATCTCGCCACTTTTGGTGCGA‑GGGGGGGGAc                            <  1:8659225/68‑1 (MQ=16)

                                         tCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACtt                          >  1:21428368/1‑68 (MQ=255)

                                         tCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACtt                          >  1:22849995/1‑68 (MQ=255)

                                         tCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACtt                          >  1:28685611/1‑68 (MQ=255)

                                           cGCCACCATCGCACACTCAACAAACAATTATTGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGa                        <  1:1141992/68‑1 (MQ=12)

                                            gCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGa                        >  1:9513564/1‑67 (MQ=255)

                                              cACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                     <  1:12412493/68‑1 (MQ=255)

                                              cACCTTCGCACAGTCATATTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAc                      >  1:12620397/1‑67 (MQ=255)

                                               aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                     >  1:2810617/1‑67 (MQ=255)

                                               aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                     >  1:17437804/1‑67 (MQ=255)

                                               aCCTTACCACATGCATCTTACTTGTTTTGAACTCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                    <  1:6886283/68‑1 (MQ=18)

                                               aCCATCGCACACTCATCTAACATTTTTTGAAATCGCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAAccc                    <  1:4527744/68‑1 (MQ=21)

                                               aCCATCGCACACGCATCATACTTTTTTTGATATCGCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAAccc                    <  1:5224897/68‑1 (MQ=25)

                                                ccTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                    >  1:5775456/1‑67 (MQ=255)

                                                    ccaacaGTCATCTAACTTTTTTTGAAATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg               <  1:23143354/65‑1 (MQ=18)

                                                    cGCACAGTCATCTTACTTTTTATGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACg               <  1:615475/68‑1 (MQ=25)

                                                     gCACAGTCATCTAACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt              <  1:24860801/68‑1 (MQ=255)

                                                     ccacaGTCATCTTACATTTTTTGAACTACCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt              <  1:18643069/67‑1 (MQ=18)

                                                     ccacaGTCATCTAACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt              <  1:14907514/67‑1 (MQ=255)

                                                      cacaGGCATCTAACTTTTTTTGAAAACCCCTATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTc             <  1:25580079/68‑1 (MQ=17)

                                                      aacaGTCATCTAACTTTTTTTGATCTCCCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTc             <  1:11685239/67‑1 (MQ=21)

                                                       acaGTCATCTTACTTTTTTTGATGTCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:6464027/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCCCGTcc            >  1:23189301/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCAGGTcc            >  1:23810869/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:18749772/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:16752521/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:15301940/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:19092327/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:29218671/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:251530/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACATGAACCCCAAAGTcc            >  1:20962064/1‑68 (MQ=37)

                                                       acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGAGA‑GGGGGGGGACTTGAACCCCCACGTcc            >  1:24430681/1‑68 (MQ=255)

                                                       acaGTCATCTTACTTTTTTTGATATAGCCTAGTTTGGTCCGA‑GGGGGCGGACTTGAACCCCCACGTcc            >  1:20044528/1‑68 (MQ=25)

                                                       acaGTCATCTTACTTTGTTTGATATCGCCTCGTTTGGAGCGA‑GGGGGGGGAATTGAAACCCCACGTcc            >  1:33410910/1‑68 (MQ=25)

                                                        cattCATCTAACTTTTTTTGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:721997/65‑1 (MQ=18)

                                                        cattCAACTAACTTTTTTTGATATACCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:10905176/65‑1 (MQ=17)

                                                        caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           >  1:10330439/1‑68 (MQ=255)

                                                         aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGt          >  1:25309094/1‑68 (MQ=255)

                                                         aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGt          >  1:495515/1‑68 (MQ=255)

                                                          gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGTGGGACTTGAACCCCCACGTCCCTa         >  1:2583589/1‑68 (MQ=255)

                                                          gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa         >  1:13762182/1‑68 (MQ=255)

                                                           tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTaa        >  1:29041869/1‑68 (MQ=255)

                                                            catcatACTTTTTTTGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:5557517/64‑1 (MQ=18)

                                                            cATGTTACTTTTTTTGATATCGCCACGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:34616042/64‑1 (MQ=255)

                                                            cATCTTACTTTTTTTGATATAGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:30716447/64‑1 (MQ=255)

                                                            cATCTTACTTTTTTGGATATCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:16868096/64‑1 (MQ=255)

                                                            cATCTAACTTTTTTTGATTTCGCCTATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:33015595/64‑1 (MQ=18)

                                                            cATCTAACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg           <  1:8277621/64‑1 (MQ=255)

                                                            cATCTAACTTTTTTTGATATCCCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa         <  1:27748828/66‑1 (MQ=255)

                                                             aTCTTACTTTTTTTGAAATCGCCTCGTTTGGGGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:26402504/68‑1 (MQ=255)

                                                             aTCTAACTTTTTTTGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:13174142/68‑1 (MQ=18)

                                                               cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:9043911/1‑68 (MQ=255)

                                                               cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:34116849/1‑68 (MQ=255)

                                                                ttACTTTTTTTGATTTCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca   <  1:26560706/68‑1 (MQ=18)

                                                                ttACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca   <  1:652535/68‑1 (MQ=255)

                                                                atACATTTATTGATCTCGCCTCGATTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca   <  1:14114971/67‑1 (MQ=17)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:31515198/1‑67 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGaaa    >  1:1955859/1‑65 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGac    >  1:30300839/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:5695687/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:23959581/1‑66 (MQ=255)

                                                                 tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:16289119/1‑66 (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: `‑`