BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,596,014	G→T	9.4%	intergenic (‑32/+3)	leuV ← / ← leuP	tRNA‑Leu/tRNA‑Leu

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,596,014	0	G	T	9.4%	921.3 / 5.4	366	intergenic (‑32/+3)	leuV/leuP	tRNA‑Leu/tRNA‑Leu
Reads supporting (aligned to +/- strand): ref base G (174/128); new base T (2/43); total (176/190)
Fisher's exact test for biased strand distribution p-value = 1.10e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 381 total aligned reads displayed.

TGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCG  >  CP009273/4595947‑4596080

tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                                     <  1:23496516/68‑1 (MQ=255)

tGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCg                                                                     <  1:30260944/68‑1 (MQ=255)

 gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGt                                                                    <  1:5886750/68‑1 (MQ=255)

 gAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGt                                                                    <  1:36458791/68‑1 (MQ=255)

   aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGACTCGttt                                                                  >  1:31103015/1‑68 (MQ=255)

   aGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGGCTCATTACTTTTATTGATATGGGCTCggtg                                                                  >  1:5259858/1‑65 (MQ=17)

     cTAGCGCGTCTACCAATTCCGCCACCTTCGCCCAGTCATCTTACTTTTTTTGATATAGCCTCGTTTgg                                                                >  1:18106627/1‑68 (MQ=255)

     cTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                                                >  1:43511893/1‑68 (MQ=255)

     cTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                                                >  1:31498855/1‑68 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTTATATCGCCTCGTTTGGt                                                               <  1:36215839/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTgg                                                                <  1:26250181/67‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTg                                                                 <  1:38678300/66‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:13985428/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:34187673/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:32264573/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:41825760/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:16035116/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:2524339/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:10871744/68‑1 (MQ=255)

      tAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGt                                                               <  1:28326919/68‑1 (MQ=255)

         cgcgTCTACCAATTCCGCCACCTTCGCAGAGTCAGCTTACTTTTTTTGATATCGCCTCGGgtggtggc                                                            >  1:35726290/1‑66 (MQ=25)

            gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑g                                                         <  1:23269316/67‑1 (MQ=255)

            gTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑g                                                         <  1:21153616/67‑1 (MQ=255)

            gTCTACCAATTCCGCCACCTTCGCACAGGCATCTTACATTTTTTGATATCGCCTCGTTTGGTGCGA‑g                                                         <  1:10006937/67‑1 (MQ=38)

              cTACCAATTCCGCCACCTTCTCACAGTCATCTTACTTTTTTTGATATCCCCTCGTTTGGTGCGA‑ggg                                                       <  1:9067899/67‑1 (MQ=39)

               tACCAATTCCGCCACCTTCGCACAGTCATCTTACATTTTTTGATATCGCCTCGTTTGGTGCGA‑ggggg                                                     <  1:5611393/68‑1 (MQ=255)

                aCCAATTCCGCCACCTTCGCACAGTCATCTTACTTTATTTGATATCGCCTCGTTTGGTGCGA‑gggggg                                                    <  1:10243803/68‑1 (MQ=255)

                      tCCGCCACCTTCGCACAGACATATTTCTTTATTTGATATCGACGCGGTGGGTGCGA‑GGGGTGGGGCtt                                              >  1:12675837/1‑68 (MQ=255)

                        cGCCACCTACGCACAGGCATCTTACTTTATTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGa                                            <  1:12009982/68‑1 (MQ=38)

                           cACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAc                                          >  1:17708591/1‑67 (MQ=255)

                           cACCATCCCACATTCATCATACATTTTTTGATATAGCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAAcc                                         <  1:39383310/68‑1 (MQ=21)

                            acattCGCACAGTCATATTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGAATTGAAcc                                         >  1:29231422/4‑67 (MQ=38)

                            aacTTCGCACAGTCATCAAACTTTTATTGAAATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAccc                                        <  1:24083552/66‑1 (MQ=25)

                            aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                                         >  1:20757845/1‑67 (MQ=255)

                            aCCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAAcc                                         >  1:25522983/1‑67 (MQ=255)

                            aCCTTCCCACAGTCATCTTACTATAATTGATATCCCCTCGATTGGTGCGA‑GGGGGGGGACTTGAAccc                                        <  1:4880487/68‑1 (MQ=21)

                            aCCTACCCACAGTCATCTTACATTTTATGAAATCCCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAAccc                                        <  1:24621401/68‑1 (MQ=18)

                                 cccacaTTCATCTTACATTTTTTGATCTCCCCTCTTTTGGGGCGA‑GGGGGGGGACTTGAACCCCCACg                                   <  1:42349372/66‑1 (MQ=18)

                                  tcacaGTCATCAAACTTTTTTTGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt                                  <  1:5147942/67‑1 (MQ=21)

                                   cacaTTCAACTAACATTTTTTGATTTCGCCAAGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTc                                 <  1:33919642/68‑1 (MQ=17)

                                   cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt                                  >  1:14444247/1‑67 (MQ=255)

                                   cacaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGt                                  >  1:13753325/1‑67 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:25869970/1‑68 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:1054315/1‑68 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:38809184/1‑68 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:23615685/1‑68 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:34384025/1‑68 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:20961347/1‑68 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:33169966/1‑68 (MQ=255)

                                    acaGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:25487341/1‑68 (MQ=255)

                                    acaGTCATCTTACATTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                >  1:34932705/1‑68 (MQ=255)

                                    acaGTCATCTAACTATATTTGAAATACCCACGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTcc                                <  1:20500428/68‑1 (MQ=17)

                                      aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGAGGGGGGGGGACTTGAACCCCCACGTCCg                               >  1:11854089/1‑68 (MQ=255)

                                      aGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGt                              >  1:2376616/1‑68 (MQ=255)

                                        tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTaa                            >  1:4520237/1‑68 (MQ=255)

                                        tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTaa                            >  1:38350365/1‑68 (MQ=255)

                                        tCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGAATTGAACCCCCACGTCCGTaa                            >  1:11073856/1‑68 (MQ=255)

                                         cATCTTACTTTTTTTTATTTCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCg                               <  1:40246653/64‑1 (MQ=255)

                                         cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTaa                            <  1:38909531/67‑1 (MQ=255)

                                         cATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAg                           >  1:19603101/1‑68 (MQ=255)

                                         cATCTAACATTTTTTGATTTCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTa                             <  1:28881870/66‑1 (MQ=17)

                                          aacTTAATTTTTTTGTTATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTTAACCCCCACGTCCGTAAGa                          <  1:21415402/66‑1 (MQ=18)

                                           tCTTACTTTTTTTGATATCGCCTCGTTGGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGaa                         <  1:16483102/68‑1 (MQ=255)

                                           acTTACTTTTTTTGATATCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGaa                         <  1:30495021/67‑1 (MQ=255)

                                            cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGCac                        >  1:12381475/1‑68 (MQ=255)

                                            cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:1528777/1‑68 (MQ=255)

                                            cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:4293518/1‑68 (MQ=255)

                                            cTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:41286221/1‑68 (MQ=255)

                                             ttACTTTTTTTGATATCGCCTCGTTTGGTGCGC‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca                       <  1:11290770/68‑1 (MQ=255)

                                             aaaCTTTTTTTGATTTCCCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAaca                       <  1:22770334/66‑1 (MQ=18)

                                              tccTTTTTTTGAACTCCCCTCCTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAacac                      <  1:34712836/66‑1 (MQ=17)

                                              tccTTTTATTTACATCGCCGCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGacac                      <  1:8235383/66‑1 (MQ=14)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:33664884/1‑66 (MQ=255)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:21835030/1‑66 (MQ=255)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:22550514/1‑66 (MQ=255)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:31820044/1‑66 (MQ=255)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:32894658/1‑66 (MQ=255)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:19050524/1‑66 (MQ=255)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:32066237/1‑66 (MQ=255)

                                              tACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAac                        >  1:650670/1‑66 (MQ=255)

                                              tACTTTATTTGATATACCCACGTTTGGGGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAacac                      <  1:42699607/68‑1 (MQ=17)

                                               aCTTTTTTTGATCTATCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACt                     <  1:7791244/68‑1 (MQ=17)

                                                cTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa                    >  1:16860417/1‑68 (MQ=255)

                                                cTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTa                    >  1:40925111/1‑68 (MQ=255)

                                                  ttttttGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGCCTTGAACCCCCACGTCCGTAAGAACACTAac                  >  1:37432521/1‑68 (MQ=255)

                                                   tttttGATATCGCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca                 <  1:36921962/68‑1 (MQ=255)

                                                   tttttGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGCACCCCCACGTCCGTAAGAACACTAaca                 <  1:18548935/68‑1 (MQ=255)

                                                   tttttGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca                 <  1:6620033/68‑1 (MQ=255)

                                                   ttattGATTTCGCGTATTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAaca                 <  1:26564461/65‑1 (MQ=11)

                                                     tttGATCTCCCCACTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc               <  1:28106268/68‑1 (MQ=14)

                                                     tttGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc               <  1:43079173/68‑1 (MQ=255)

                                                     tttGATATCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc               <  1:24479095/68‑1 (MQ=255)

                                                     tttGATATAACCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc               <  1:15668986/68‑1 (MQ=14)

                                                     tttCATATCGCCGCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGGACACTAACAcc               <  1:43301903/68‑1 (MQ=14)

                                                     tatGATATCTCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc               <  1:30588518/66‑1 (MQ=14)

                                                     attGATATCTCCTTGATTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACAcc               <  1:628394/67‑1 (MQ=14)

                                                         atatCGCCTCGTTTGGTGCGA‑GGTGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa           >  1:6996778/1‑68 (MQ=255)

                                                         atatCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa           >  1:27579099/1‑68 (MQ=255)

                                                         atatCCCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGaa           <  1:1300388/68‑1 (MQ=255)

                                                            tagCCTCTTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCt        <  1:10756314/66‑1 (MQ=255)

TGAAGCTAGCGCGTCTACCAATTCCGCCACCTTCGCACAGTCATCTTACTTTTTTTGATATCGCCTCGTTTGGTGCGA‑GGGGGGGGACTTGAACCCCCACGTCCGTAAGAACACTAACACCTGAAGCTAGCGCG  >  CP009273/4595947‑4596080

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: `‑`