Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,907,534 G→A N15N (AAC→AAT)  phoU ← negative regulator of the pho regulon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,907,5340GA98.3% 211.1 / NA 60N15N (AAC→AAT) phoUnegative regulator of the pho regulon
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (26/33);  total (27/33)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGAACAGATCGTCCGTG  >  NC_000913/3907397‑3907662
                                                                                                                                         |                                                                                                                                
aCGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCAtt                                                                                                                                >  1:869045/1‑140 (MQ=255)
   ttCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCAGATACTTTCCAGTTCGGCATTGaa                                                                                                                             <  1:374343/140‑1 (MQ=255)
       tGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTgg                                                                                                                         >  2:666555/1‑140 (MQ=255)
        gTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGc                                                                                                                        <  1:232520/140‑1 (MQ=255)
              ttCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGaaa                                                                                                                  <  2:27379/140‑1 (MQ=255)
                cGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAata                                                                                                                >  1:929286/1‑140 (MQ=255)
                  aTGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATg                                                                                                              <  1:53165/140‑1 (MQ=255)
                      cgcgCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTtta                                                                                                          >  2:710708/1‑140 (MQ=255)
                        cgcTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTttatt                                                                                                        <  2:869045/140‑1 (MQ=255)
                                  gATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCGCCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTgaga                                                                                              <  1:815104/140‑1 (MQ=255)
                                    tCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACt                                                                                            <  2:27193/140‑1 (MQ=255)
                                     cGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTg                                                                                           >  1:681983/1‑140 (MQ=255)
                                       cTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTc                                                                                         >  2:239532/1‑140 (MQ=255)
                                         gTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCa                                                                                       <  2:63388/140‑1 (MQ=255)
                                         gTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCa                                                                                       <  1:710708/140‑1 (MQ=255)
                                             tGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAAc                                                                                   >  2:765063/1‑140 (MQ=255)
                                              ggTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACg                                                                                  <  1:417523/140‑1 (MQ=255)
                                              ggTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACg                                                                                  <  1:239532/140‑1 (MQ=255)
                                              ggTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACg                                                                                  <  2:191589/140‑1 (MQ=255)
                                               gTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTgaga                                                                                              >  2:103751/1‑127 (MQ=255)
                                               gTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTgaga                                                                                              <  1:103751/127‑1 (MQ=255)
                                               gTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGc                                                                                 <  1:697301/140‑1 (MQ=255)
                                                ttATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCa                                                                                <  1:206718/140‑1 (MQ=255)
                                                ttATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCa                                                                                <  2:929286/140‑1 (MQ=255)
                                                  aTGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTgaga                                                                                              <  2:929698/124‑1 (MQ=255)
                                                  aTGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTgaga                                                                                              >  1:929698/1‑124 (MQ=255)
                                                       tCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGa                                                                         <  1:81070/140‑1 (MQ=255)
                                                         gcgGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACg                                                                                  <  1:445299/129‑1 (MQ=255)
                                                         gcgGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACg                                                                                  >  2:445299/1‑129 (MQ=255)
                                                         gcgGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAAt                                                                       >  1:919496/1‑140 (MQ=255)
                                                         gcgGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAAt                                                                       >  2:217086/1‑140 (MQ=255)
                                                          cgGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATc                                                                      >  1:82093/1‑140 (MQ=255)
                                                          cgGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATc                                                                      >  2:723602/1‑140 (MQ=255)
                                                          cgGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATc                                                                      >  1:613632/1‑140 (MQ=255)
                                                                      cAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGAc                                                          <  2:836213/140‑1 (MQ=255)
                                                                      cAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGAc                                                          <  2:613632/140‑1 (MQ=255)
                                                                        gAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCg                                                        <  1:217086/140‑1 (MQ=255)
                                                                         aaaGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCgg                                                       >  2:649584/1‑140 (MQ=255)
                                                                         aaaGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCgg                                                       >  2:413679/1‑140 (MQ=255)
                                                                              tgctgctCCACCATGCCGCCCATGGGCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATg                                                  >  2:15609/1‑140 (MQ=255)
                                                                                          aTGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCtgtt                                      >  1:155657/1‑140 (MQ=255)
                                                                                                cccATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTttc                                >  2:790667/1‑140 (MQ=255)
                                                                                                cccATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTttc                                >  2:816374/1‑140 (MQ=255)
                                                                                                     ggTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGc                           >  1:70468/1‑140 (MQ=255)
                                                                                                       tcatcaCCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTg                         <  2:919496/140‑1 (MQ=255)
                                                                                                       tcatcaCCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTg                         <  2:681983/140‑1 (MQ=255)
                                                                                                       tcatcaCCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTg                         <  2:82093/140‑1 (MQ=255)
                                                                                                        catcaCCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTgg                        <  1:723602/140‑1 (MQ=255)
                                                                                                           caCCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCtt                     <  1:816374/140‑1 (MQ=255)
                                                                                                            aCCTGCGTGCGGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTg                    <  1:790667/140‑1 (MQ=255)
                                                                                                                gcgtgcgGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTg                    >  1:91973/1‑136 (MQ=255)
                                                                                                                gcgtgcgGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTg                    <  2:91973/136‑1 (MQ=255)
                                                                                                                 cgtgcgGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGaa               >  2:495186/1‑140 (MQ=255)
                                                                                                                   tgcgGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCg                            <  1:387935/125‑1 (MQ=255)
                                                                                                                   tgcgGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCg                            >  2:387935/1‑125 (MQ=255)
                                                                                                                   tgcgGATACTTTCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGAACa             >  1:160150/1‑140 (MQ=255)
                                                                                                                            tttCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGAACAGATCGTCCg    <  2:160150/140‑1 (MQ=255)
                                                                                                                              tCCAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGAACAGATCGTCCgtg  <  1:765063/140‑1 (MQ=255)
                                                                                                                               ccAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGAACAGATCGt       >  1:451174/1‑134 (MQ=255)
                                                                                                                               ccAGTTCGGCATTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGAACAGATCGt       <  2:451174/134‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                
ACGTTCTTGTCGCCTTCGATGACGCGCTTCGCCAGATCGCTGTCCTGGTTATGCATCGCGGTGATTGCATCAGAAAGCTGCTGCTCCACCATGCCGCCCATGGTCATCACCTGCGTGCGGATACTTTCCAGTTCGGCGTTGAACTGGCCGGAAATATGTTTATTAAGATTGAGACTGTCCATAACGCACTCCTGAATCAACCGTAACGACCGGTGATGTAGTCTTCTGTTTGTTTCTTCGCTGGCTTGGTGAACAGATCGTCCGTG  >  NC_000913/3907397‑3907662

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑