BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,595,993	T→A	6.0%	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	6.0%	1105.1 / 7.0	395	intergenic (‑11/+24)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base T (158/203); new base A (3/25); total (167/228)
Fisher's exact test for biased strand distribution p-value = 4.87e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 458 total aligned reads displayed.

GTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACAC  >  CP009273/4595926‑4596060

   cGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACt                                                                  <  1:37154149/68‑1 (MQ=255)

   cGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACt                                                                  <  1:50102628/68‑1 (MQ=255)

   cGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACt                                                                  <  1:19044684/68‑1 (MQ=255)

      aaGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCAGAGTCTGATTACtttt                                                               >  1:30345826/1‑68 (MQ=11)

        ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttttt                                                             >  1:7061404/1‑68 (MQ=255)

        ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttttt                                                             >  1:34405042/1‑68 (MQ=255)

        ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACtttttt                                                             >  1:2492613/1‑68 (MQ=255)

        ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCGGACtttatt                                                             >  1:17769199/1‑68 (MQ=14)

        ggACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACACACAAATTACttttat                                                             >  1:22735721/1‑66 (MQ=11)

          acacTAACACCTGAAGCTAGCGCGTCTACCTATTCCGCCACCTTCGCACAGTCATCTTa                                                                    >  1:7568765/1‑59 (MQ=255)

          acacTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGGCAGCTTACTTTTTTTg                                                           >  1:10641052/1‑68 (MQ=255)

            acTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGat                                                         >  1:46690354/1‑68 (MQ=255)

            acTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTAAATTTTTTTGat                                                         >  1:34181848/1‑68 (MQ=255)

                 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                    <  1:4359983/68‑1 (MQ=255)

                 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                    <  1:14417081/68‑1 (MQ=255)

                 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                    <  1:2648471/68‑1 (MQ=255)

                 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                    <  1:21931795/68‑1 (MQ=255)

                 cacCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGc                                                    <  1:21265672/68‑1 (MQ=255)

                  acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCg                                                     >  1:31251229/1‑66 (MQ=255)

                  acCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGcc                                                   <  1:11648262/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCTATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:31576504/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:37955143/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:31987400/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:35623058/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:36085749/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:39666429/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:51145514/68‑1 (MQ=255)

                     tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                <  1:20669063/68‑1 (MQ=255)

                        aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGttt                                             >  1:28144490/1‑68 (MQ=255)

                        aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGtt                                              <  1:30878558/67‑1 (MQ=255)

                        aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGtt                                              <  1:27191424/67‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:42974923/68‑1 (MQ=255)

                           tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                          <  1:27607053/68‑1 (MQ=255)

                             gcgcGTCTACCAATTCCGCCACCTTCGCACAGTCCTCTTACTTTTTTGGATATCGCCTCGGTTGGTGc                                        >  1:47600438/1‑68 (MQ=25)

                               gcgTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCg                                       <  1:38808388/67‑1 (MQ=255)

                                 gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg                                     <  1:36805205/67‑1 (MQ=255)

                                 gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAg                                     <  1:35378252/67‑1 (MQ=255)

                                   cTACCAATTCCGCCACCTTCGCACAGGCAACTAACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                   <  1:46833858/67‑1 (MQ=38)

                                        aaTTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGa                             <  1:39973508/68‑1 (MQ=255)

                                        aaTTCCGCCACCTAATCACATTGATCAAACAATTTTTGATTTCCACTCGTTTGGTGCGAGGGGGGGGa                             <  1:42771681/68‑1 (MQ=12)

                                        aaTTCCGCCACCATCGCACAGGCATCTTACATTTTTTGATATCCCCACGATTGGTGCGAGGGGGGGGa                             <  1:48709260/68‑1 (MQ=37)

                                         aTTCCGCCACCTTCGCAAAGTCAGATTACTTTATAAGATTTCGAAGCGGTTCGGGCGAggcggggg                              >  1:10263299/1‑66 (MQ=255)

                                           tCCGCCACCTTCGCAGACACAGCATTCTTTTTTTGATATCGAAACGGTTGGTGCGAGGGGAGGGAAtt                          >  1:33173724/1‑68 (MQ=255)

                                              gCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGa                        >  1:9232367/1‑67 (MQ=255)

                                                 aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAcc                     >  1:19897109/1‑67 (MQ=255)

                                                 aCCTTCGCACACTCAACTTACTTTTTATGAACTCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                    <  1:18611690/68‑1 (MQ=25)

                                                 aCCTTCCCACAGGCATCATACATTATATGATATCCCCAACTTTGGTGCGAGGGGGGGGACTTGAAccc                    <  1:20892143/68‑1 (MQ=12)

                                                 aCCTTATCACAGTCATCTTACTATTTTTGATTTCTCCTCTTTTGGTGCGAGGGGGGGGACTTGAAccc                    <  1:1214664/68‑1 (MQ=21)

                                                 aCCATCGCACAGTCATCTTACATTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                    <  1:41185364/68‑1 (MQ=255)

                                                  ccTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccc                    >  1:6371020/1‑67 (MQ=255)

                                                   cTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccccc                  >  1:24030144/1‑68 (MQ=255)

                                                      tgCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAggg                                   <  1:4168139/47‑1 (MQ=255)

                                                      ctcacaGTCATCTTACATTAATTGAAATACCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACg               <  1:14843680/66‑1 (MQ=17)

                                                      cGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACg               <  1:4021065/68‑1 (MQ=255)

                                                       gCACTGTCATCTTACTTTTTTTTATATCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt              <  1:6040323/68‑1 (MQ=21)

                                                        cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt              >  1:456979/1‑67 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGt              >  1:25327016/1‑66 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:5552684/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:45144179/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:44170544/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:18135528/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:29693354/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:38194229/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:26246073/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:29249177/1‑68 (MQ=255)

                                                         acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTcc            >  1:23646649/1‑68 (MQ=255)

                                                          caGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           >  1:50403726/1‑68 (MQ=255)

                                                            gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         >  1:42486381/1‑68 (MQ=255)

                                                            gTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTa         >  1:48546105/1‑68 (MQ=255)

                                                              cATCTTACTTTTTTTGATCTCGCCTCCTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           <  1:23165882/64‑1 (MQ=255)

                                                              cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           <  1:4901068/64‑1 (MQ=255)

                                                              cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           <  1:13797974/64‑1 (MQ=255)

                                                              cATCTAACTTTTTTTGATCTCCCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           <  1:44432153/64‑1 (MQ=18)

                                                              cATCTAACTTTTATTGATATCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           <  1:49426156/64‑1 (MQ=18)

                                                              cATCTAACTTTTATTGATATCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCg           <  1:13288770/64‑1 (MQ=18)

                                                               accTTACTATATTTCAAAACGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAgg      <  1:6621997/66‑2 (MQ=14)

                                                               aTCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:40717033/68‑1 (MQ=255)

                                                               aTCTTACTTTTTTTGAAATTGCCACTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGa      <  1:20122919/68‑1 (MQ=17)

                                                                tCTTACTTTTTTTGATATCCCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGaa     <  1:8491674/68‑1 (MQ=255)

                                                                tCTTACTTTTTTGGATATCCCCACGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGaa     <  1:1289527/68‑1 (MQ=18)

                                                                 cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:29034444/1‑68 (MQ=255)

                                                                 cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:11228391/1‑68 (MQ=255)

                                                                  ttACTTTTTTTGATATCGCCTCTTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca   <  1:15139956/68‑1 (MQ=255)

                                                                  ttACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAacg   <  1:7300333/68‑2 (MQ=255)

                                                                  atACATTTTTTGAAATACCCTAGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca   <  1:45862835/67‑1 (MQ=17)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAAccccc                  >  1:16447244/1‑52 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAacac  <  1:40826937/68‑1 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:19283821/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:8175976/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:28740469/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:29798485/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:12591003/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:32607306/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:33516705/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:16177618/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:17268109/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:41558696/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:20472584/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAac    >  1:37663279/1‑66 (MQ=255)

                                                                   tACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGACCGTAAGAac    >  1:10082959/1‑66 (MQ=255)

GTCCGTAAGGACACTAACACCTGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGACTTGAACCCCCACGTCCGTAAGAACAC  >  CP009273/4595926‑4596060

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: `‑`