Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,790,152 C→T 9.2% intergenic (+31/+37) ynfM → / ← PP_5073 efflux transporter/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,790,1520CT 9.2% 147.8 / 4.5 54intergenic (+31/+37)ynfM/PP_5073efflux transporter/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/25);  new base T (2/3);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.85e-01

TTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGGTGTCGG  >  NC_002947/5790011‑5790293
                                                                                                                                               |                                                                                                                                               
ttCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGa                                                                                                                                          <  2:168518/149‑1 (MQ=255)
      cACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACACCCGCTCCCACAGGTTGTGGGT‑‑GCgggc                                                                                                                                  <  6:23364/149‑2 (MQ=39)
           gTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAGCCTGTGGGA‑‑GCGGGTGTGAc                                                                                                                             >  6:29573/1‑149 (MQ=255)
           gTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGAc                                                                                                                             <  7:288229/149‑1 (MQ=255)
                    gAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCATGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAagag                                                                                                                    <  8:232593/149‑1 (MQ=255)
                    gAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAagag                                                                                                                    <  3:189759/149‑1 (MQ=255)
                      aCGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGCCTCATTGCACCACATCCAGCTGCCACCCAAAACGGTGTGATGCATTCCTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAaga                                                                                                                     <  1:112387/148‑1 (MQ=255)
                         ggATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCAGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCat                                                                                                               <  5:254766/149‑1 (MQ=255)
                            tCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑g                                                                                                                                       <  7:20060/122‑1 (MQ=255)
                            tCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCat                                                                                                               >  4:318270/1‑146 (MQ=255)
                            tCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTCTGGGA‑‑g                                                                                                                                       >  8:20060/1‑122 (MQ=255)
                              gggCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGGG‑‑GCGTGGCACCTGAGCAAGTTGCCACCCAAAACGGGGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCatcagat                                                                                                          <  1:175562/149‑1 (MQ=255)
                                  tGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCatcagat                                                                                                          <  8:82889/145‑1 (MQ=255)
                                  tGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCatcagat                                                                                                          >  7:82889/1‑145 (MQ=255)
                                       aTTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAGCCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTtgatg                                                                                                 <  5:29573/149‑1 (MQ=255)
                                         tGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTgatgat                                                                                               >  7:43620/1‑149 (MQ=255)
                                             aGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGCGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                                >  6:250612/1‑112 (MQ=255)
                                             aGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGCGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                                <  5:250612/112‑1 (MQ=255)
                                                      gCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatcc                                                                                  <  3:344682/149‑1 (MQ=255)
                                                            gCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacatc                                                                             >  5:1905/1‑148 (MQ=255)
                                                             cgttGATGGTG‑‑GCGTTGCAGCTGAGCAAGTTGCCACCCAAAACGGTTTGATGCATTCGTGGGCACGCGCGCACCCACAACCTGTGGGACCTCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacacc                                                                             <  1:100149/147‑3 (MQ=255)
                                                                     gtg‑‑gCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                                >  2:170206/1‑88 (MQ=255)
                                                                     gtg‑‑gCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                                <  1:170206/88‑1 (MQ=255)
                                                                     gtg‑‑gCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCg                                                                    <  6:1905/148‑1 (MQ=255)
                                                                                     gAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCtt                                                     >  8:133379/1‑149 (MQ=255)
                                                                                      aGCAAGTTGCCACCCAAAACGTTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatc                                                                                   <  3:269461/118‑1 (MQ=255)
                                                                                      aGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatc                                                                                   >  4:269461/1‑118 (MQ=255)
                                                                                           gTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGtc                                                        >  2:292926/1‑139 (MQ=255)
                                                                                            ttGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAAcc                                              <  2:286231/149‑1 (MQ=255)
                                                                                                  cccAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAAAATCCACATCCACTTCCCGGCTCATCATGTGCTTTTAAACCTAAcc                                         >  8:46462/1‑148 (MQ=255)
                                                                                                    cAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGt                                      >  6:341973/1‑149 (MQ=255)
                                                                                                     aaaaCGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTc                                     <  7:133379/149‑1 (MQ=255)
                                                                                                         cGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCt                                 <  8:43620/149‑1 (MQ=255)
                                                                                                            tgtgATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacatc                                                                             <  2:24530/102‑1 (MQ=255)
                                                                                                            tgtgATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacatc                                                                             >  1:24530/1‑102 (MQ=255)
                                                                                                                  gCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTACTTTTCAACCTCACCGGTCAGCTTCACCTTgg                        >  4:202676/1‑149 (MQ=255)
                                                                                                                   cATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTgg                        >  4:255997/1‑148 (MQ=255)
                                                                                                                      tCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCtt                    >  5:325792/1‑149 (MQ=255)
                                                                                                                       cGTGGTCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCtt                    <  7:46462/148‑1 (MQ=255)
                                                                                                                       cGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTg                   >  5:130094/1‑149 (MQ=255)
                                                                                                                        gTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGt                  <  6:325792/149‑1 (MQ=255)
                                                                                                                          ggtcacaCCCGCTCCCACAGGTTGTGGGT‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCg                >  8:160097/4‑149 (MQ=38)
                                                                                                                           ggCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGt               >  3:72539/1‑149 (MQ=255)
                                                                                                                           ggCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGt               <  6:130094/149‑1 (MQ=255)
                                                                                                                             cacaCCCGCTCCCACAGGTTGTGGGT‑‑GCGGGCGTGCCCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTc                                     >  6:60566/1‑125 (MQ=37)
                                                                                                                             cacaCCCGCTCCCACAGGTTGTGGGT‑‑GCGGGCGTGCCCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTc                                     <  5:60566/125‑1 (MQ=37)
                                                                                                                              acacccGCTCCCACAGGTTGTGGGT‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGa            <  7:160097/146‑1 (MQ=39)
                                                                                                                                  ccGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGGCTTGTCGTTTCACgg        >  6:164805/1‑149 (MQ=255)
                                                                                                                                    gCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTCCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGgtg      <  3:202676/149‑1 (MQ=255)
                                                                                                                                        ccACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTg                         >  2:167504/1‑126 (MQ=255)
                                                                                                                                        ccACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTg                         <  1:167504/126‑1 (MQ=255)
                                                                                                                                        ccACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGGTGTcgg  >  1:342944/1‑149 (MQ=255)
                                                                                                                                        ccACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACATCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGGTGTcgg  >  5:72018/1‑149 (MQ=255)
                                                                                                                                            aaCCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacatc                                                                             >  8:18087/1‑70 (MQ=255)
                                                                                                                                               |                                                                                                                                               
TTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGGTGTCGG  >  NC_002947/5790011‑5790293

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑