Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,747,351 T→A 13.4% E53V (GAG→GTG)  PP_5473 ← LuxR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,747,3510TA13.4% 100.3 / 6.4 50E53V (GAG→GTG) PP_5473LuxR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (14/27);  new base A (5/2);  total (21/29)
Fisher's exact test for biased strand distribution p-value = 9.67e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.55e-01

GGTGCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACCTTGA  >  NC_002947/1747203‑1747498
                                                                                                                                                     |                                                                                                                                                    
ggTGCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑t                                                                                                                                                      >  6:235829/1‑149 (MQ=255)
     gcgcCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGAAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGgc                                                                                                                                                 <  5:41990/149‑1 (MQ=255)
      cgcCAGGAGCGGCTGTAGCGTGTCCACCTTCGCTTGGAAGGCCGTTTGCATTGTTGTGTGCATGGATGATCCTCGGGTGGGTCAGGCGGGGTATTCGATGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGgcg                                                                                                                                                <  3:266489/149‑1 (MQ=21)
           ggAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCgcgg                                                                                                                                           >  4:18011/1‑149 (MQ=255)
            gAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCgcggc                                                                                                                                          >  4:138485/1‑149 (MQ=255)
             aGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCgcggcg                                                                                                                                         <  4:274910/149‑1 (MQ=255)
             aGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCgcggcg                                                                                                                                         <  2:264812/149‑1 (MQ=255)
                          tgtCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATg                                                                                                                            <  2:56435/149‑1 (MQ=255)
                            tCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATggg                                                                                                                          <  3:18011/149‑1 (MQ=255)
                              cACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCgcgg                                                                                                                                  <  6:225670/139‑1 (MQ=255)
                              cACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCgcgg                                                                                                                                  >  5:225670/1‑139 (MQ=255)
                              cACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCCCCCC‑ACCCGCGCGCGGCGGTCGCGGGGCAAGGGGt                                                                                                                        >  4:98666/1‑149 (MQ=21)
                               aCCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑AGCGGCGCGCCGCGGTCGCGGCGCATGGGGtt                                                                                                                       >  3:182711/1‑148 (MQ=255)
                               aCCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCCC‑TCCGGAGCGCGGCGGTAGCGGCGCATGTGGta                                                                                                                       >  5:149896/1‑148 (MQ=255)
                                ccTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATTATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCg                                                                                                                      <  5:150687/149‑1 (MQ=255)
                                     tctTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGG‑AGCGgcgcaccgc                                                                                                                                          >  1:243054/1‑119 (MQ=18)
                                     tctTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGG‑AGCGgcgcaccgc                                                                                                                                          <  2:243054/124‑6 (MQ=18)
                                     tctTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCCCGGCGGTCGCGGCGCCTGGGGTAGCTGTc                                                                                                                 >  4:31463/1‑149 (MQ=255)
                                     tctTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCCC‑GACCGCGCCCGGCGGGGGCGGCGCAAGGGGTGGCTGtg                                                                                                                 >  4:156365/1‑148 (MQ=18)
                                                  ggTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGgca                                                                                                    <  3:98666/149‑1 (MQ=255)
                                                  ggTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCCGCGCATGGGGTCGCTGTCGTTGATGGCGgca                                                                                                    >  6:307193/1‑149 (MQ=255)
                                                   gTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TACGGCGCGCGGCGGTCGCGGCGCATGGGGGCGATGTAGTTGATggcggc                                                                                                     >  4:77795/1‑147 (MQ=255)
                                                     gCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑GACGGCCCGCGGCGGTCGCGGCGCATGGGGTCGCGGTCGTTGATGGCGgcatt                                                                                                  >  8:287740/1‑147 (MQ=255)
                                                       aTTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATgg                                                                                                                           <  5:258962/121‑1 (MQ=255)
                                                       aTTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATgg                                                                                                                           >  6:258962/1‑121 (MQ=255)
                                                       aTTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGgcatgcat                                                                                               >  2:67705/1‑149 (MQ=255)
                                                              tgtGCTTGGATGATCCTCGGGTGGGTCTGGCGTGGGATTCGAATGCCTCGGCCTTACGAACGATTTGAACTTGGGCGGTGCGGCGC‑TCCTGCGCGCGGCGGTCGCGGCGCATGGGGTCGATGTCGTTGATGGCGGCATGCATTGCcaca                                                                                        <  6:212713/147‑1 (MQ=17)
                                                                   aTGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAagaca                                                                                   <  4:104960/149‑1 (MQ=255)
                                                                   aTGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCGCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAagaca                                                                                   <  1:83095/149‑1 (MQ=255)
                                                                      gatgatCGTCGGGTGGGTCAGGCTTGGTATTCGAAGGCCTGGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGGATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAagacaga‑c                                                                               <  6:149896/149‑1 (MQ=255)
                                                                          atCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAgg                                                                           <  3:138485/149‑1 (MQ=255)
                                                                                gggtgggtCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGa                                                                       <  1:8176/147‑1 (MQ=255)
                                                                                gggtgggtCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAgg                                                                     <  3:156365/149‑1 (MQ=255)
                                                                                  gtgggtCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCGTGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCa                                                                   <  2:163827/149‑1 (MQ=255)
                                                                                       tCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCAAGGGGTCGCTGTGGTTGATGGCGGCATGCATTGCCCCAAGACAGA‑CCCGGGCGAGGCACAGCg                                                              >  6:123377/1‑149 (MQ=21)
                                                                                            cGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTGGTTGATGGCGGCCTGCATTGGCACAAGACAGA‑CCAGGGCGAGGCagaagatggg                                                          >  7:149406/1‑141 (MQ=21)
                                                                                            cGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCag                                                                  <  8:149406/140‑1 (MQ=255)
                                                                                                  ttcgtaaGGCCGAGGCCTT‑CGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCCTTCAATGCCACAAGCCCGA‑CCAGGGCGAGGCAGAGCGGAGTTTTGAtct                                                  >  2:210280/6‑149 (MQ=21)
                                                                                                     cGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGAtctt                                                 <  3:31463/148‑1 (MQ=255)
                                                                                                       aaGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGa                                                            <  3:47245/135‑1 (MQ=255)
                                                                                                                      cgaacgaTTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGACCCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTTGTATGCCGCctct                                 <  1:67705/148‑1 (MQ=255)
                                                                                                                       gaacgaTTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGGCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCt                              <  2:97265/149‑1 (MQ=255)
                                                                                                                          cgaTTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACg                           <  5:307193/149‑1 (MQ=255)
                                                                                                                           gaTTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACga                          <  7:287740/149‑1 (MQ=255)
                                                                                                                             ttCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCTGAGTGATGATCTTCTGGTATGCCGCCTCTGc                               <  1:166449/142‑1 (MQ=255)
                                                                                                                                        cccatGCGCCGCGACCGCCGCGCGCCGG‑AGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGtgatga                                                     <  7:231214/105‑1 (MQ=25)
                                                                                                                                        cccatGCGCCGCGACCGCCGCGCGCCGG‑AGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGtgatga                                                     >  8:231214/5‑109 (MQ=25)
                                                                                                                                           gTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGc           >  2:224060/1‑148 (MQ=255)
                                                                                                                                           atGCGCCGCGACCGCCGCGCGCCGG‑AGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGc           >  6:32654/2‑148 (MQ=255)
                                                                                                                                                 cgc‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACCtt    >  7:61660/1‑149 (MQ=255)
                                                                                                                                                   c‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACCTTGa  <  5:123377/149‑1 (MQ=255)
                                                                                                                                                     |                                                                                                                                                    
GGTGCGCGCCAGGAGCGCCTTTAGCGTGTCCACCTTCTCTTGGAAGGCCGGGTGCATTGTTGTCTGCATGGATGATCCTCGGGTGGGTCAGGCGTGGTATTCGAAGGCCTCGGCCTTACGAACGATTCGAACTTGGGCGGTGCGCCGC‑TCCGGCGCGCGGCGGTCGCGGCGCATGGGGTCGCTGTCGTTGATGGCGGCATGCATTGCCACAAGACAGA‑CCAGGGCGAGGCAGAGCGGAGTGATGATCTTCTGGTATGCCGCCTCTGCTACGAGAGCAGTTCGACGGCGAACCTTGA  >  NC_002947/1747203‑1747498

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑