Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,266,162 C→A 7.7% V99V (GTG→GTT)  PP_3738 ← transcriptional regulator VanR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,266,1620CA 7.7% 162.7 / 3.7 52V99V (GTG→GTT) PP_3738transcriptional regulator VanR
Reads supporting (aligned to +/- strand):  ref base C (25/23);  new base A (2/2);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

TGGCTGGCGTCGATGATCACCTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGCCACCAAAGCGCACCAGCAGGCCTTCCTGTTCG  >  NC_002947/4266025‑4266309
                                                                                                                                          |                                                                                                                                                   
tggctggcGTCGATGATCACCTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGcc                                                                                                                                          <  6:96338/149‑1 (MQ=255)
tggctggcGTCGATGATCACCTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGc                                                                                                                                           <  3:54228/148‑1 (MQ=255)
  gctggcGTCGATGATCACCTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCAc                                                                                                                                        >  1:88973/1‑149 (MQ=255)
            atgatCACCTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGc                                                                                                                              >  2:211619/1‑149 (MQ=255)
             tgatCACCTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGAGCGTGCTTGCACCGACAAGCCACGTTCTGCAGcc                                                                                                                             >  5:9658/1‑149 (MQ=255)
                    cTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGc                                                                                                                                                     >  1:255063/1‑118 (MQ=255)
                    cTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGc                                                                                                                                                     <  2:255063/118‑1 (MQ=255)
                      gatgaAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGcgcc                                                                                                                    >  6:106274/1‑149 (MQ=255)
                            aGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCt                                                                                                                            >  5:187184/1‑135 (MQ=255)
                            aGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCt                                                                                                                            <  6:187184/135‑1 (MQ=255)
                            aGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAAc                                                                                                              <  2:88973/149‑1 (MQ=255)
                            aGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAAc                                                                                                              <  3:181611/149‑1 (MQ=255)
                              cgcATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGAACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAAccc                                                                                                            >  1:1334/1‑149 (MQ=255)
                              cgcATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGAACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAAccc                                                                                                            >  1:6874/1‑149 (MQ=255)
                                   gTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCt                                                                                                                                   <  7:142778/121‑1 (MQ=255)
                                   gTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCt                                                                                                                                   >  8:142778/1‑121 (MQ=255)
                                    ttCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCa                                                                                                       <  5:106274/148‑1 (MQ=255)
                                    ttCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAg                                                                                                      <  3:237481/149‑1 (MQ=255)
                                     tCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACAA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCa                                                                                                                                >  4:221211/1‑122 (MQ=255)
                                       aGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGcac                                                                                                   <  1:211619/149‑1 (MQ=255)
                                              gATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCgcgc                                                                                            >  8:267924/1‑149 (MQ=255)
                                               aTAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCa                                                                                                       <  6:40130/137‑1 (MQ=255)
                                               aTAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCa                                                                                                       >  5:40130/1‑137 (MQ=255)
                                                   aCCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTc                                                                                       >  4:117518/1‑149 (MQ=255)
                                                     cTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGAACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGa                                                                                     <  2:1334/149‑1 (MQ=255)
                                                     cTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGAACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGa                                                                                     <  2:6874/149‑1 (MQ=255)
                                                      tGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGcc                                                                                                                             >  8:142940/1‑108 (MQ=255)
                                                      tGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGcc                                                                                                                             <  7:142940/108‑1 (MQ=255)
                                                       gCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGAcc                                                                                   >  3:94815/1‑149 (MQ=255)
                                                          aGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCa                                                                                <  7:267924/149‑1 (MQ=255)
                                                           gtcgtcTGCGCTCACAAAGCCCTAGTCGAACAGCTGAGCGCCGGCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCAc                                                                               <  8:157489/149‑1 (MQ=255)
                                                               tcTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCcgc                                                                           <  4:94815/149‑1 (MQ=255)
                                                                   cGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGAt                                                                        <  4:476/148‑1 (MQ=255)
                                                                     cTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCgcgc                                                                                            >  8:242762/1‑126 (MQ=255)
                                                                     cTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCgcgc                                                                                            <  7:242762/126‑1 (MQ=255)
                                                                       caacaatgcctggtcgacggcgatcagctgttcgacAAGGGCTTTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCa                                                                    >  1:248046‑M2/37‑149 (MQ=255)
                                                                              cccTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCCACGCAGCGCGTGCTTGCACCGACACGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGAGCACCTCTACCGCACCCGCGAGGTCATCGGCGCt                                                            >  4:18564/1‑149 (MQ=255)
                                                                                ctggtcgacggcgatcagctgttcgacCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCa                                                                                                                                >  7:121043‑M2/28‑79 (MQ=255)
                                                                                ctggtcgacggcgatcagctgttcgacCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCa                                                                                                                                <  8:121043‑M2/52‑1 (MQ=255)
                                                                                ctggtcgacggcgatcagctgttcgacCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGc                                                                                                     >  2:87673‑M2/28‑106 (MQ=255)
                                                                                ctggtcgacggcgatcagctgttcgacCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGc                                                                                                     <  1:87673‑M2/79‑1 (MQ=255)
                                                                                    TCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGa                                                      >  3:117518‑M1/1‑149 (MQ=255)
                                                                                          aGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAAc                                                                                                              >  8:178860/1‑87 (MQ=255)
                                                                                          aGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAAc                                                                                                              <  7:178860/87‑1 (MQ=255)
                                                                                                tCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGaaa                                          <  2:195430/149‑1 (MQ=255)
                                                                                                    cGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAAcccc                                      >  2:13129/1‑149 (MQ=255)
                                                                                                        gacCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGc                                  >  7:97946‑M2/4‑149 (MQ=255)
                                                                                                         acCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCg                                    >  7:261072‑M2/3‑146 (MQ=255)
                                                                                                         acCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCCCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCg                                    <  8:261072‑M2/144‑1 (MQ=255)
                                                                                                            a‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGccac                               >  6:42177/1‑148 (MQ=255)
                                                                                                                        cAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGCCACCAAAGCGCACca                   <  8:97946/149‑1 (MQ=255)
                                                                                                                         aaCGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGAGGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGc                                  >  1:242904/1‑133 (MQ=255)
                                                                                                                         aaCGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGc                                  <  2:242904/133‑1 (MQ=255)
                                                                                                                                 gcgTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGCCACCAAAGCGCACCAGCAGGCCtt          >  3:235316/1‑149 (MQ=255)
                                                                                                                                          cACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGCCACCAAAGCGCACCAGCAGGCCTTCCTGTTCg  <  8:230030/148‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                                   
TGGCTGGCGTCGATGATCACCTGATGAAAGCGCATGTTCAGGTCGTGATAGACCTGCAAGTCGTCTTCGCTCACAAAGCCCTTGTCGAACAGCTGATCGCCGTCGACCA‑GGCATTGTTGCAACGCAGCGCGTGCTTGCACCGACAAGCCACGTTCTGCAGCCTGACGCGCCGCCAACCCCTCCAGCACACCGCGCACCTCGACCGCACCCGCGATGTCATCGGCGCTGACCGAGCGCACCTGAAACCCCCGGCCACCAAAGCGCACCAGCAGGCCTTCCTGTTCG  >  NC_002947/4266025‑4266309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑