BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,382,371	G→T	9.3%	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	9.3%	971.4 / 11.5	364	intergenic (+7/‑29)	glyX/glyY	tRNA‑Gly/tRNA‑Gly
Reads supporting (aligned to +/- strand): ref base G (98/215); new base T (16/24); total (114/250)
Fisher's exact test for biased strand distribution p-value = 2.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 364 total aligned reads displayed.

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAg                                                            >  1:6982522/1‑68 (MQ=14)

tAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAg                                                            >  1:34099706/1‑68 (MQ=31)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:31288797/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:16725604/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:10827633/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           >  1:22916702/1‑68 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:7339599/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:12501822/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:33809239/68‑1 (MQ=33)

 agagCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           <  1:19531426/68‑1 (MQ=33)

    gCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGc                                                         <  1:865586/67‑1 (MQ=37)

     cACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGt                                                           >  1:36506587/1‑64 (MQ=33)

      ccGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      >  1:320391/2‑68 (MQ=255)

      aCGACCTTGCCCAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:9288398/68‑1 (MQ=255)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:20275689/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:32899321/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:23144705/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:17001536/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCt                                                        <  1:20781832/66‑1 (MQ=39)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:18252729/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      >  1:31040202/1‑68 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:2534287/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:30900782/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:26404724/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:26558255/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:6468768/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:3035121/68‑1 (MQ=40)

      aCGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGt                                                      <  1:28695156/68‑1 (MQ=40)

        gACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTaa                                                    <  1:24801455/68‑1 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAATTTTGAAAGTGCTTTAAg                                                   >  1:6258516/1‑68 (MQ=255)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAATTGATGTAAg                                                   >  1:14497051/1‑68 (MQ=11)

         aCCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTGTAAg                                                   >  1:14688460/1‑68 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:9665270/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:13364054/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:13775949/68‑1 (MQ=255)

          ccTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAgg                                                  <  1:5553885/68‑1 (MQ=255)

           cTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGc                                                 <  1:35579765/68‑1 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                              >  1:21586349/1‑68 (MQ=255)

              gCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGcaca                                              <  1:35797617/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGCTTTAATTCACAg                                             >  1:1001407/1‑67 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGGGCTGTAAGGAACAg                                             >  1:3173094/1‑67 (MQ=17)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGATAGTGCTGTAAGGGACAg                                             >  1:2912449/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGATAGTGATGTAATGCACAg                                             >  1:4631852/1‑67 (MQ=14)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAg                                             >  1:13157888/1‑67 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:23886591/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:27365546/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:30494705/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            <  1:22647607/68‑1 (MQ=255)

                cAAGGTCGGGGTCGCGAGATCGAGTCTCGTATCCCCCTCCAAAATTTGCAAGTCCTATAAGCCACAg                                             >  1:11532512/1‑67 (MQ=14)

                 aaGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGa                                            >  1:33416784/1‑67 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                          <  1:33063971/68‑1 (MQ=255)

                  aGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGacc                                          <  1:27833169/68‑1 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTGATGTAAGGCACAGacca                                         >  1:29213905/1‑67 (MQ=255)

                    gTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTTAAAGAGATGTAAGGAACAGagca                                         >  1:28213079/1‑67 (MQ=14)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:603255/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccac                                        <  1:17402791/67‑1 (MQ=255)

                     tCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATATTAAAGAGATTTAATGAACAGaccac                                        >  1:33527125/1‑67 (MQ=14)

                      cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGaccacc                                       <  1:14067545/67‑1 (MQ=255)

                      cGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCAccc                                      <  1:27025371/68‑1 (MQ=255)

                         ggTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCaa                                    <  1:30098810/67‑1 (MQ=255)

                          ggcgcgAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:23976679/65‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTTATTTAATGAACAGACCACCCAAGc                                  >  1:1171282/1‑68 (MQ=14)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:29497231/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:20610727/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:1268027/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:28985165/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:24218443/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAg                                   <  1:24454635/67‑1 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGc                                  >  1:2797796/1‑68 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGAACAGACCCCCCAAGc                                  >  1:234058/1‑68 (MQ=255)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGATATAAGGCACAGACCACCCAAga                                  >  1:26006681/1‑67 (MQ=17)

                          gTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGAGCTGTAATGCACAGACCACCCAAGc                                  >  1:3964075/1‑68 (MQ=255)

                              cgAGTTCGAGTGTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGAAAGGCACAGACCACCCAAGCggg                               <  1:77046/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:3668404/67‑1 (MQ=255)

                               gAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGa                              <  1:19961153/67‑1 (MQ=255)

                                 gTTCTAGTCTCGTTTCCCGCTCCAAAATTTTAAAGTTCTGTAAGGCACAGACCACCCAAGCGGGTAt                            <  1:5457823/67‑1 (MQ=17)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                           <  1:5195973/66‑1 (MQ=255)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATa                           <  1:21253555/66‑1 (MQ=255)

                                   tCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGc                         <  1:12014125/68‑1 (MQ=255)

                                     gAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTc                       <  1:34552231/68‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:14197746/66‑1 (MQ=255)

                                         ctcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:15952796/66‑1 (MQ=255)

                                         ctcGTTTCCCGCGCCAAAATTTTAAAGTGCTGAAAGTCACAGACCACCCAAGCGGGAATAGCTCAg                     <  1:28423644/66‑1 (MQ=14)

                                         ctcGTTGCCCGCTCCAAAAATTGAAAGGGGTGTAAGGGACAGACCACGCAAGCGGGAATTGCTCAg                     <  1:22023654/66‑1 (MQ=17)

                                         cgcGTTACCCGCTCCAAAATTTTAAAGTCCTGAAAGGCACAGACCACCCAAGCGGGAATAGCTCAGtt                   <  1:31949757/66‑1 (MQ=14)

                                         cccGTTTCCCGCGCCAAAATTTTAAATTGCGGTACCTCACAGACCTCCCAAGCGGGAATAGCTCAGtt                   <  1:36160982/66‑1 (MQ=9)

                                          tcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTg                  <  1:35085642/68‑1 (MQ=255)

                                          tcGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTg                  <  1:22618451/68‑1 (MQ=255)

                                             tttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGTATAGCGCAGTTGGTa               >  1:11202355/1‑68 (MQ=255)

                                              ttCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGtcg              >  1:30581823/1‑66 (MQ=255)

                                               tCCCGCTCCAAAATTTTAAAGTTCTGTAAGGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:32421759/68‑1 (MQ=17)

                                               tCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:13438513/68‑1 (MQ=255)

                                               tCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             >  1:1013321/1‑68 (MQ=255)

                                               tCCCCCTCCAAAATTTTAAAGTGCGGAACGGCACAGACCACCCACGCGGGAATAGCTCAGTTGGTaga             <  1:18617811/68‑1 (MQ=14)

                                               tCCAGCACCAAAATTTTAAAGTGCTGTAACGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTaga             <  1:10395273/68‑1 (MQ=14)

                                                 ccGCTCCAAAATTTTAAAGTGCTGAAACTCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGc           <  1:15012249/68‑1 (MQ=14)

                                                     gccAAAATTTTAAAGTCCTGAACCGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGa       <  1:19137381/67‑1 (MQ=14)

                                                      cgaaaaTGTGAAAGTGCTGTAACGCACATACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc      <  1:13614957/66‑1 (MQ=14)

                                                      caaaaaTTTCAAAGTGCTGAAACGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGAc      <  1:8962304/66‑1 (MQ=11)

                                                          aaTTTAAAAGTTCTTTAACGAACATACCAAGCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTg  <  1:15535599/68‑1 (MQ=14)

TAGAGCACGACCTTGCCAAGGTCGGGGTCGCGAGTTCGAGTCTCGTTTCCCGCTCCAAAATTTGAAAGTGCTGTAAGGCACAGACCACCCAAGCGGGAATAGCTCAGTTGGTAGAGCACGACCTTG  >  CP009273/4382308‑4382433

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: `‑`