BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,381	T→A	6.2%	intergenic (+17/‑19)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,382,381	0	T	A	6.2%	756.6 / 5.8	294	intergenic (+17/‑19)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base T (85/188); new base A (2/19); total (87/207)
Fisher's exact test for biased strand distribution p-value = 4.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 314 total aligned reads displayed.

ACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTC  >  CP009273/4382314‑4382447

aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                                    >  1:2520314/1‑68 (MQ=40)

aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                                    <  1:17628555/68‑1 (MQ=40)

aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                                    <  1:10935763/68‑1 (MQ=40)

aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                                    <  1:3305436/68‑1 (MQ=40)

aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                                    <  1:537818/68‑1 (MQ=40)

aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGt                                                                    >  1:829623/1‑68 (MQ=255)

  gACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTaa                                                                  <  1:13114665/68‑1 (MQ=255)

   aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGAGATGTaat                                                                 >  1:18646874/1‑67 (MQ=11)

   aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGTGATGTAAg                                                                 >  1:13749874/1‑68 (MQ=255)

    ccTTGCCAAGGTCGTGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:29350995/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTaatg                                                                >  1:4230057/1‑66 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:2729606/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:16352347/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:34029515/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:14938442/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:516646/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:22739700/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:25390969/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:10719429/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:24165092/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                                 >  1:7511827/1‑67 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                                 >  1:32468287/1‑67 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGATTCCCGCTCCAAAATTTGAAAGTGCAGTAAgg                                                                <  1:1904716/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGTCGAGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:14087712/68‑1 (MQ=255)

    ccTTGCCAAGGTCGGGGGCGCGAGTTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGGGCTGTACgg                                                                <  1:8551255/68‑1 (MQ=14)

    ccTTGACAAGGGCTGGGTCGCGAGTTCGAGTCTCGTTTACCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:23268415/68‑1 (MQ=17)

    ccTTCCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                                <  1:25628168/68‑1 (MQ=255)

     cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                               <  1:10044282/68‑1 (MQ=255)

     cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                               <  1:19729626/68‑1 (MQ=255)

     cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                               >  1:31780056/1‑68 (MQ=255)

         ccAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAATGaacac                                                           >  1:34235190/1‑67 (MQ=14)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTGTAAGGCACAg                                                           >  1:24846481/1‑67 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGATAGTGCTGTAAGGCACAg                                                           >  1:18079570/1‑67 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTTTAATGCACAg                                                           >  1:31947346/1‑67 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                           >  1:15991908/1‑67 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                           >  1:2768661/1‑67 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                           >  1:24283145/1‑67 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                          <  1:26330454/68‑1 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                          <  1:5901148/68‑1 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                          <  1:22915938/68‑1 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                          <  1:7322008/68‑1 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                          <  1:10557517/68‑1 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                                          <  1:19371380/68‑1 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAAGGAACAg                                                           >  1:11676391/1‑67 (MQ=255)

          cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATGAAAGTGCTGTAAGGCACAg                                                           >  1:5973590/1‑67 (MQ=255)

            aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                                        <  1:14406994/68‑1 (MQ=255)

               tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                                      <  1:9525462/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAACGTGCTGTAAGGAACACACCACCCAAGc                                                >  1:14597806/1‑68 (MQ=17)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:30885299/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:30142775/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:7834693/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:33521934/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:28257822/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:33866476/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:14456604/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:26243046/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                                 <  1:22394773/67‑1 (MQ=255)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGTAAGGCACAGACCGCCCCAGc                                                >  1:6158280/1‑68 (MQ=17)

                    gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATTAAAGTGATGAAAGGAACAGACCACCCAAGc                                                >  1:3511242/1‑68 (MQ=14)

                    gTCGCGAGTTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGTGCGGTAAGGCACAGACCACCCAAg                                                 <  1:27255938/67‑1 (MQ=17)

                     tCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGc                                                <  1:9450161/67‑1 (MQ=255)

                      cgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCgg                                              <  1:9241569/68‑1 (MQ=255)

                       gcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCggg                                             <  1:8112832/68‑1 (MQ=255)

                         tatttCGAGTCTCGTTTCCCGCTACAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                            <  1:31600530/64‑1 (MQ=17)

                         gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                            <  1:4411008/67‑1 (MQ=255)

                         gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                            <  1:23898260/67‑1 (MQ=255)

                         gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                            <  1:9011229/67‑1 (MQ=255)

                         gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAACGCACAGACCACCCAAGCGGGa                                            <  1:11814997/67‑1 (MQ=255)

                           tttCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                         <  1:11208701/67‑1 (MQ=255)

                             tCGAGTCTCGTTTCCCGGGCCAAAATTTAAAAGTGCTGTAAGTCACAGACCACCCAAGCGGGAATa                                         <  1:5004151/66‑1 (MQ=14)

                             tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                                         <  1:31274464/66‑1 (MQ=255)

                               gAGTCTCGTTACCCGCTCCAAAATTTTAAAGTGCTGAAACTCACAGACCACCCAAGCGGGAATAGCTc                                     <  1:17873671/68‑1 (MQ=14)

                                aGTCTCGTTTCCCGCTCCAAAATTTTAAAGGACTATAAGGAACAGACCGCCCACGAGGGTATAGcgga                                    >  1:28476626/1‑65 (MQ=12)

                                   ctcGTTTCGCGATCGAAAATTTTAAAGTGCGGTAAGGCAAAGACCACCCAAGCGGGAATAGCTCAg                                   <  1:12658282/66‑1 (MQ=17)

                                   ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAg                                   <  1:3690451/66‑1 (MQ=17)

                                   ctcGTTTCCCGCTCCAAAATTTGAAAGTTCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                   <  1:25036727/66‑1 (MQ=255)

                                   ctcGTTTCCCGCTCCAAAATTTCAAAGTGCGGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                   <  1:12210466/66‑1 (MQ=255)

                                   ctcGTTTCCCGCACCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                                   <  1:13144883/66‑1 (MQ=255)

                                   ctcGTTACCCGCTCCAAAATTTGAAAGTTCTGAAAGTCACAGACCACCCAAGCGGGAATAGCTCAGtt                                 <  1:137220/68‑1 (MQ=14)

                                   cgcGTTTCCCGGTCCAAAATTTTAAATTGCTGTAAGGAACAGACCACCCACGCGGGAATAGCTCAg                                   <  1:29698484/64‑1 (MQ=17)

                                      gTTTCCCGCTCCAAAATTTGAAAGTGCTTTAAGTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGt                              <  1:29235566/68‑1 (MQ=255)

                                      gTTTCCCCCTCGAAATTTTTAAAGTGCTGTAACTAACATACCACCCAAGCGGGAATAGCTCAGTTGGt                              <  1:29909320/68‑1 (MQ=14)

                                       tttCCCGCTCCAAAATTTGAAAGTGATGTAATTACCAGACCAACCAAGCGGGTATAGCGCAGTTGGTa                             >  1:22171839/1‑68 (MQ=14)

                                        ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTag                            >  1:15395086/1‑68 (MQ=255)

                                         tCCCGGGCCAAAATTTTAAAGTTCGGTAAGGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTaga                           <  1:16913746/68‑1 (MQ=17)

                                         tCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                           <  1:15027517/68‑1 (MQ=255)

                                         tCCCGCTCCAAAATTTCAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                           <  1:21586854/68‑1 (MQ=255)

                                          cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                           >  1:4258747/1‑67 (MQ=255)

                                          cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                           >  1:23487284/1‑67 (MQ=255)

                                            cGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTAAGTTGGTAGAGc                         >  1:16119408/1‑67 (MQ=255)

                                               cccAAAATTTTAAAGTGCTGAAAGGAACATACCACCCACGCGGGAATAGCTCAGTTGGTAGAGCACGa                     <  1:26994309/67‑1 (MQ=14)

                                               cagaaaaTTTTAAAGTGCTCTAACGCACAGACCAACCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa                     <  1:20705608/65‑1 (MQ=14)

                                                ccAAAATTTTAAACAGCTGTAACTCACAGACCACCTAAGCGGGAATAGCTCAGTTGGTAGACCACGAc                    <  1:20160883/68‑1 (MQ=14)

                                                ccAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc                    <  1:6728366/68‑1 (MQ=255)

                                                    aaTTTTAAAGTGCGCTAACTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGCAGAGCACGACCTTg                <  1:27959648/68‑1 (MQ=14)

                                                    aaTTTGAAAGTTCTGTAAGGCACATACGACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                <  1:32326658/68‑1 (MQ=17)

                                                    aaTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                <  1:17395652/68‑1 (MQ=255)

                                                    aaTTTGAAAGTCCTGAAACGCACAGACCACCCACGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                <  1:32736431/68‑1 (MQ=14)

                                                     aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg                >  1:10292988/1‑67 (MQ=255)

                                                                  gTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTc  >  1:18853494/1‑68 (MQ=39)

ACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGTC  >  CP009273/4382314‑4382447

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: `‑`