Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,516,689	T→C	100%	T382A (ACG→GCG)	yfeA ←	putative diguanylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,516,689	0	T	C	100.0%	259.9 / ‑6.7	78	T382A (ACG→GCG)	yfeA	putative diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (45/32);  minor base G (1/0);  total (46/32)

GTCGCCCTTCCGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGTACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCGCAGGCAGCAAAAACTCT  >  NC_000913/2516593‑2516784                                                                                                 |                                                                                                gTCGCCCTTCCGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACg                                                                                              >  2:1249413/1‑100 (MQ=255)   cGCCCTTCCGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACg                                                                                              >  2:2180967/1‑98 (MQ=255)    gaccTTCCGTTTCAGGCCCGCTCAGCACTAAAAGCAGTTCACGACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCa                                                                                           >  1:1510948/3‑100 (MQ=255)      ccTTCCGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCaaa                                                                                         <  1:2139063/100‑1 (MQ=255)       cTTCCGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAAt                                                                                        >  1:930017/1‑100 (MQ=255)        ttCCGTTTCCGGCCCGCTTAGCACTAACAGCAGTTCACTTCCCGGCAATTGTTACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAAtt                                                                                       <  2:1923215/100‑1 (MQ=255)         tCCGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTg                                                                                      <  1:718158/100‑1 (MQ=255)          ccGTTTCCGGCCCGCTAAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCTGACGGCaaaat                                                                                       >  2:1759660/1‑96 (MQ=255)           cGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAg                                                                                    >  1:939355/1‑100 (MQ=255)           cGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAg                                                                                    >  1:383338/1‑100 (MQ=255)           cGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAg                                                                                    >  2:2041582/1‑100 (MQ=255)           cGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAg                                                                                    >  1:1758181/1‑100 (MQ=255)            gTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAg                                                                                    >  2:587036/1‑99 (MQ=255)            gTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTACCTGCATCAACGGCAGCAGCGCACGGCAAATTGAg                                                                                    >  1:518792/1‑99 (MQ=255)             tttCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCg                                                                                  <  1:922538/100‑1 (MQ=255)             tttCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCg                                                                                  <  1:1546268/100‑1 (MQ=255)             tttCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCg                                                                                  <  1:427776/100‑1 (MQ=255)             tttCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTACCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCg                                                                                  <  2:518793/100‑1 (MQ=255)              ttCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCgg                                                                                 >  1:1638150/1‑100 (MQ=255)              ttCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCgg                                                                                 >  1:1638094/1‑100 (MQ=255)               tCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGa                                                                                >  2:1425038/1‑100 (MQ=255)               tCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGa                                                                                <  2:608359/100‑1 (MQ=255)                ccGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGAt                                                                               >  1:1409441/1‑100 (MQ=255)                  ggCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATAc                                                                             >  1:1930477/1‑100 (MQ=255)                  ggCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATAc                                                                             <  1:2155005/100‑1 (MQ=255)                    cccGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAg                                                                           >  2:1181819/1‑100 (MQ=255)                    cccGCTCAGCACTAACAGCAGTTCACTACCCGGCAAGTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAg                                                                           >  1:1580608/1‑100 (MQ=255)                     ccGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGt                                                                          <  1:479535/100‑1 (MQ=255)                       gCTCAGCACTAACAGCATTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGTGCACGGCAAATTGAGCGGATACAGTGa                                                                        <  2:866368/100‑1 (MQ=255)                       gCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGa                                                                        >  2:566015/1‑100 (MQ=255)                         tCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAAc                                                                      <  2:321818/100‑1 (MQ=255)                          cAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAAcg                                                                     <  1:874344/100‑1 (MQ=255)                            gCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAAcgcg                                                                   >  1:2159461/1‑100 (MQ=255)                            gCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAAcgcg                                                                   >  1:1988718/1‑100 (MQ=255)                            gCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAAcgcg                                                                   >  1:1980951/1‑100 (MQ=255)                              aCTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGca                                                                 <  2:1923279/100‑1 (MQ=255)                              aCTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGca                                                                 >  2:168641/1‑100 (MQ=255)                               cTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACgcgc                                                                  <  2:498988/98‑1 (MQ=255)                                 aaCAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGcatca                                                              >  2:188047/1‑100 (MQ=255)                                  aCAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGCGCGGATACAGTGAACGCGcatcat                                                             >  2:1464591/1‑100 (MQ=255)                                   cagcagTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCAtt                                                            >  2:1748559/1‑100 (MQ=255)                                      cagTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAg                                                         >  2:607365/1‑100 (MQ=255)                                       agTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGc                                                        <  1:1804048/100‑1 (MQ=255)                                        gTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGcc                                                       >  2:192637/1‑100 (MQ=255)                                          tCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGt                                                     >  2:391806/1‑100 (MQ=255)                                          tCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGt                                                     >  2:1820632/1‑100 (MQ=255)                                           cACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCACATCATTAAGCCGTa                                                    >  2:709234/1‑100 (MQ=255)                                                cccGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATgac                                               >  1:2188393/1‑100 (MQ=255)                                                   ggCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATgacgac                                            <  2:1795795/100‑1 (MQ=255)                                                   ggCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATgacgac                                            <  2:1795807/100‑1 (MQ=255)                                                     cAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATgacgac                                            <  1:1696508/98‑1 (MQ=255)                                                      aaTTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGTCGACTCa                                         <  1:1177636/100‑1 (MQ=255)                                                          gATACAACTTGTCGTTATCATGCATCAACGGCAGCAGCACACGACAAATTAAGCGTATACAGTGAACGCGCAGCATTAAGCCGTAATgacgcataa                                         >  2:1234126/1‑91 (MQ=255)                                                           aTACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATaaa                                     >  1:956444/1‑99 (MQ=255)                                                           aTACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAAc                                    >  2:543806/1‑100 (MQ=255)                                                              cAACTTTTCGGTTTCCTGCATCAACGGCAGCAGCGCCCGGCAAATTGAGCGGATAAAGTGAAAGCGCATCATTAAGCGGTAATGACTACTCATAAACTCa                                 >  2:1719416/1‑100 (MQ=255)                                                               aaCTTTTCGTTCTCCTCCATCAACGGCACCAGCGCACGACAAATTGAGAGGATAAATTGAACTCGCATCATTAAGCCGTAATGAAGACACAAAAAGTCaa                                <  2:232225/100‑1 (MQ=255)                                                                 cTTTTCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGa                              >  1:527508/1‑100 (MQ=255)                                                                   tttCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGAtt                            >  2:160402/1‑100 (MQ=255)                                                                   tttCGTTTTCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGAtt                            >  1:1097510/1‑100 (MQ=255)                                                                        ttttCCTGCATCAACGGTAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCaa                       <  2:449330/100‑1 (MQ=255)                                                                        ttttCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCaa                       >  1:1435134/1‑100 (MQ=255)                                                                         tttCCTCCCTTAACTCCAGCATCTCACCGCAAATTGAACTCATACAGTAAACGCGCATCATTAATCCTTAAAAACGACTCATAAACTCAATATTATCaa                       <  2:1988360/99‑1 (MQ=255)                                                                           tCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATgc                    >  1:1194231/1‑100 (MQ=255)                                                                           tCCTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGAGCATCATTACGCCGTAATGACAACTCATAAACCCAATATTACCaa                       >  2:1868395/1‑97 (MQ=255)                                                                           tCCTGCATCAACGGCAGCAGAGCACGGCAAATTGAGCGGATACAGTGAACGCGCAACAATAAGCCGTAATGACGACTCATAAACTCAAGATTATCaa                       >  2:1092546/1‑97 (MQ=255)                                                                            ccTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATgcg                   <  1:117165/100‑1 (MQ=255)                                                                             cTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATgcgc                  <  1:366189/100‑1 (MQ=255)                                                                             cTGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATgcgc                  >  2:636618/1‑100 (MQ=255)                                                                              tGCATCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCgca                 <  2:1444934/100‑1 (MQ=255)                                                                                 aTCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCgcaggc              >  2:215556/1‑100 (MQ=255)                                                                                 aTCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCgcaggc              <  1:1177376/100‑1 (MQ=255)                                                                                  tCAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCgcaggca             <  1:1820644/100‑1 (MQ=255)                                                                                   cAACGGCAGCAGCGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTATTGACGACTCATAAACTCAAGATTATCAATGCgcaggcag            >  2:1948181/1‑100 (MQ=255)                                                                                   cAACGGCAGCAGCGCACGGCAAATTGAGCGGAGACAGTGAACGCGCATCATGAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCgcaggcag            <  2:2038118/100‑1 (MQ=255)                                                                                        gcaacagcGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCGCAGGCAGCaaaa       <  1:1683502/96‑1 (MQ=255)                                                                                           gcagcGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCGCAGGCAGCAAAAAct    <  1:1506075/100‑1 (MQ=255)                                                                                             agcGCACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCGCAGGCAGCAAAAActct  <  1:239063/100‑1 (MQ=255)                                                                                                 |                                                                                                GTCGCCCTTCCGTTTCCGGCCCGCTCAGCACTAACAGCAGTTCACTACCCGGCAATTGATACAACTTTTCGTTTTCCTGCATCAACGGCAGCAGCGTACGGCAAATTGAGCGGATACAGTGAACGCGCATCATTAAGCCGTAATGACGACTCATAAACTCAAGATTATCAATGCGCAGGCAGCAAAAACTCT  >  NC_000913/2516593‑2516784

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑