BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	10.9%	intergenic (+7/‑29)	glyX → / → glyY	tRNA‑Gly/tRNA‑Gly

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,382,371	0	G	T	10.9%	972.5 / 16.0	385	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (92/224); new base T (17/29); total (109/276)
Fisher's exact test for biased strand distribution p-value = 3.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 386 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCA  >  CP009273/4382308‑4382436

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                               >  1:37580297/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                               >  1:34522892/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                               >  1:19745596/1‑68 (MQ=31)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGACTCGTTTCCCGCTCAAAAATTTGAAAg                                                               >  1:10017462/1‑68 (MQ=255)

 atagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                              <  1:35196335/66‑1 (MQ=18)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                              >  1:10078926/1‑68 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                              <  1:9293994/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                              <  1:24069197/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                              <  1:17385047/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                              >  1:16972416/1‑68 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                              <  1:15598162/68‑1 (MQ=33)

  gagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTg                                                             >  1:32134566/1‑68 (MQ=35)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                            <  1:5739786/67‑1 (MQ=37)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTGt                                                         >  1:6940839/1‑68 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGGGCttt                                                         >  1:37847782/1‑66 (MQ=11)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                           <  1:28115792/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                           <  1:21656531/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                           <  1:12053514/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                           <  1:7511062/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         <  1:8350986/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         >  1:32957626/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         <  1:14150900/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         >  1:2154868/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         <  1:38708698/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         <  1:18856420/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         <  1:29640824/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         <  1:8928788/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                         <  1:29167208/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGt                                                         >  1:24651092/1‑68 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTACCCGCTCCAAAATTTGAAAGTGCTGt                                                         >  1:8053236/1‑68 (MQ=255)

        gACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTaa                                                       >  1:2514958/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAg                                                      >  1:22311298/1‑68 (MQ=255)

         aCCTGGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGGTAGGGCTGTAAg                                                      >  1:28327811/1‑68 (MQ=11)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATGTaat                                                      >  1:22522294/1‑66 (MQ=14)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                     <  1:5066736/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                     <  1:561087/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                     <  1:14486779/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                     <  1:23196621/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGGTCGAGTCTCGTGTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                     <  1:19385994/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                    <  1:34213708/68‑1 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                                 <  1:15377954/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCTAGTCTCGTTTCCCGCTACAAAATTTTAAAGTGATGTAAGCCACAg                                                >  1:27391301/1‑67 (MQ=17)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAATGaacac                                                >  1:24447001/1‑66 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGAACAg                                                >  1:33861284/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATGTAAGGAACAg                                                >  1:31232097/1‑67 (MQ=17)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCCCAg                                                >  1:13472799/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                                >  1:6307345/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                               <  1:3896305/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                               <  1:17992025/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                               <  1:17698881/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATGAAATGCACAg                                                >  1:30431235/1‑67 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGAGCTGTAAGGCACAg                                                >  1:30115929/1‑67 (MQ=255)

                   ggTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGCAAGTTATGTAAGGGACAGacc                                             >  1:9145693/1‑67 (MQ=17)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTAGAAACTGCTGGAAGGCACAGccca                                            >  1:13675023/1‑67 (MQ=14)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                           >  1:35800315/1‑67 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacca                                            <  1:12754016/66‑1 (MQ=255)

                      cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCAccc                                         <  1:18444841/68‑1 (MQ=255)

                          ggcgcgAGTGCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:4436868/65‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTTCTTTAATGAACAGACCCCCCAGGc                                     >  1:27132267/1‑68 (MQ=14)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:36167086/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:4256974/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:39371493/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:38271236/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:27888758/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:32032534/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:26832578/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGc                                     >  1:20065301/1‑68 (MQ=255)

                          gTCGCGAGTGCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                      <  1:28776320/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                 <  1:24881986/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                 <  1:15885445/67‑1 (MQ=255)

                               gAGTTCGAGGCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                                 <  1:6178481/67‑1 (MQ=255)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAATTTCTGTAATTCACACACCGCCCAAGAGGGAATAGc                            >  1:29268278/1‑68 (MQ=14)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                            <  1:20676044/68‑1 (MQ=255)

                                       gTCTCGTTACCCGCTACAAAATTTAAAAGTGCTGAAACTCACATACCACCCAAGCGGGAATAGCTCAg                        <  1:10922690/68‑1 (MQ=11)

                                        tctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGAGGGAATAGCGCAGt                       >  1:6632314/1‑68 (MQ=255)

                                         ctcGTTTCCCGCTCCAAATTTTTAAAGTGCTGTAAGTCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:16429505/66‑1 (MQ=17)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:26300193/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                      <  1:11272500/68‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:31616234/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:36922586/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:23362608/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCGGTACGGCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:16714692/66‑1 (MQ=255)

                                         ctcGTATCCCGCTACAAAATTTTAAAGTTCTTTAACTCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:25569873/66‑1 (MQ=14)

                                         cgcGTTACCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                        <  1:3107656/64‑1 (MQ=255)

                                          tcGTTTCCCGCTCAAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                      <  1:34646521/67‑1 (MQ=255)

                                           cGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTgg                    <  1:18605283/68‑1 (MQ=255)

                                              ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTag                 >  1:16197895/1‑68 (MQ=255)

                                                cgcGCTACAAAATTTAAAAGTTCTTTAACTAACATACCACCCAAGCGGGAATAGCTCAGTTGGTagag               <  1:26487344/66‑1 (MQ=9)

                                                cccGCTCCAAAATTTGGAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCt                           >  1:33591347/1‑56 (MQ=255)

                                                cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                >  1:14629415/1‑67 (MQ=255)

                                                cccGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga                >  1:13330802/1‑67 (MQ=255)

                                                 ccGCTCCAAAATTTGAAAGTGCGGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc              <  1:21734/68‑1 (MQ=255)

                                                     tCCAAAATTTTAAATTTCTGTAAGTAACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa          <  1:19834985/68‑1 (MQ=17)

                                                      ccAAATTTTGAAAGTGCTGTACGTCACAGACCACCCACGCGGGAATAGCTCAGTTGGTAGAGCACGAc         <  1:10385943/68‑1 (MQ=17)

                                                      ccAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc         <  1:13066367/68‑1 (MQ=255)

                                                      ccAAAATTTAAAATTGCTTTACGAAACAGACCAACGACGCGGGAATAGCTCAGTTGGTAGAGCACGAc         <  1:25427245/68‑1 (MQ=9)

                                                      ccAAAATATCAAAGTGCTGAACGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc         <  1:11434520/68‑1 (MQ=14)

                                                       cAAAATTTCAAAGTGCTGAAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc         <  1:28856127/67‑1 (MQ=255)

                                                          attttCAAAGTGCGGAAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg     <  1:14856222/66‑1 (MQ=11)

                                                           aTTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg     >  1:12879880/1‑67 (MQ=255)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCA  >  CP009273/4382308‑4382436

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: `‑`