Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 632,127 A→C 12.5% intergenic (+128/‑55) cstA → / → ybdD carbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913632,1270AC12.5% 196.8 / 20.6 64intergenic (+128/‑55)cstA/ybdDcarbon starvation protein involved in peptide utilization; APC peptide transporter family protein/DUF466 family protein
Reads supporting (aligned to +/- strand):  ref base A (27/29);  new base C (4/4);  total (31/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

CAAAAGGCGCACACTAAAGTCAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAGGCGGCGAAGCTGATGATTGGTATGC  >  NC_000913/631983‑632248
                                                                                                                                                |                                                                                                                         
cAAAAGGCGCACACTAAAGTCAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGc                                                                                                                        >  3:345555/1‑148 (MQ=255)
cAAAAGGCGCACACTAAAGTCAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGc                                                                                                                        <  4:345555/148‑1 (MQ=255)
  aaaGGCGCACACTAAAGTCAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGt                                                                                                                      <  3:601821/148‑1 (MQ=255)
             cTAAAGTCAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           <  2:824181/132‑1 (MQ=255)
             cTAAAGTCAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           >  1:824181/1‑132 (MQ=255)
                    cAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCAcg                                                                                                                 <  4:491258/135‑1 (MQ=255)
                    cAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCAcg                                                                                                                 >  3:491258/1‑135 (MQ=255)
                       agTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcctt                                                                                                             <  3:249305/136‑3 (MQ=39)
                       agTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcctt                                                                                                             >  4:249305/1‑134 (MQ=39)
                              gggggATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCAcgc                                                                                                                >  4:69452/1‑126 (MQ=255)
                              gggggATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCAcgc                                                                                                                <  3:69452/126‑1 (MQ=255)
                                                    cTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           >  4:942981/1‑93 (MQ=255)
                                                    cTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           <  3:942981/93‑1 (MQ=255)
                                                    cTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATC                                                                                                          <  1:303469‑M1/110‑1 (MQ=255)
                                                    cTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATC                                                                                                          >  2:303469‑M1/1‑110 (MQ=255)
                                                            ccAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcc                                                                                                               >  1:352210/1‑97 (MQ=37)
                                                            ccAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcc                                                                                                               <  2:352210/97‑1 (MQ=37)
                                                             cAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCAT                                                                                                           <  4:395699‑M1/100‑1 (MQ=255)
                                                             cAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCAT                                                                                                           >  3:395699‑M1/1‑100 (MQ=255)
                                                                   tCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGt                                                                                                                      >  2:1093342/1‑83 (MQ=255)
                                                                   tCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGt                                                                                                                      <  1:1093342/83‑1 (MQ=255)
                                                                      ctctCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCAcg                                                                                                                 >  2:161321/1‑85 (MQ=255)
                                                                      ctctCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCAcg                                                                                                                 <  1:161321/85‑1 (MQ=255)
                                                                        ctcACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAgg                                                                                                                         <  3:990813/75‑1 (MQ=255)
                                                                        ctcACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAgg                                                                                                                         >  4:990813/1‑75 (MQ=255)
                                                                            cccTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCaa                                                                                         >  3:674548/1‑103 (MQ=255)
                                                                            cccTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCaa                                                                                         <  4:674548/103‑1 (MQ=255)
                                                                              cTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCC                                                                                                         <  1:585437‑M1/85‑1 (MQ=255)
                                                                              cTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCC                                                                                                         >  2:585437‑M1/1‑85 (MQ=255)
                                                                                   ccTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           >  2:1111447/1‑62 (MQ=255)
                                                                                   ccTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           <  1:1111447/62‑1 (MQ=255)
                                                                                    ctctCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcctta                                                                                                            <  1:1042840/76‑4 (MQ=37)
                                                                                    ctctCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcctta                                                                                                            >  2:1042840/1‑73 (MQ=37)
                                                                                    ctctCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcctta                                                                                                            <  3:702912/76‑4 (MQ=37)
                                                                                    ctctCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATGCGGCGTGAAcgcctta                                                                                                            >  4:702912/1‑73 (MQ=37)
                                                                                    ctctCCCCAGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGt                                                                 >  4:1113561/1‑119 (MQ=255)
                                                                                    ctctCCCCAGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGt                                                                 <  3:1113561/119‑1 (MQ=255)
                                                                                     tctcCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCgg                                                                             <  4:1140843/106‑1 (MQ=255)
                                                                                     tctcCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCgg                                                                             >  3:1140843/1‑106 (MQ=255)
                                                                                      ctcCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           <  2:199180/59‑1 (MQ=255)
                                                                                      ctcCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATaa                                                                                                                           >  1:199180/1‑59 (MQ=255)
                                                                                          ccGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCG                                                                                                        >  4:567659‑M1/1‑74 (MQ=255)
                                                                                          ccGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCG                                                                                                        <  3:567659‑M1/74‑1 (MQ=255)
                                                                                                    gAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAGGCGGCGa                    <  1:1079109/148‑1 (MQ=255)
                                                                                                        ggACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACt                                                       >  3:616934/1‑109 (MQ=255)
                                                                                                        ggACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACt                                                       <  4:616934/109‑1 (MQ=255)
                                                                                                          aCTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAg                                                                                <  4:294859/82‑1 (MQ=255)
                                                                                                          aCTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAg                                                                                >  3:294859/1‑82 (MQ=255)
                                                                                                                        ttGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAGGCGGCGAAGCTgatgat          <  3:354164/138‑1 (MQ=255)
                                                                                                                        ttGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAGGCGGCGAAGCTgatgat          >  4:354164/1‑138 (MQ=255)
                                                                                                                         tGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCAc                                                        <  3:25499/91‑1 (MQ=255)
                                                                                                                         tGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCAc                                                        >  4:25499/1‑91 (MQ=255)
                                                                                                                               cATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTc                                                                                              <  1:29501/47‑1 (MQ=255)
                                                                                                                               cATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTc                                                                                              >  2:29501/1‑47 (MQ=255)
                                                                                                                                 tttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAgg                          >  4:62758/1‑113 (MQ=255)
                                                                                                                                 tttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAgg                          <  3:62758/113‑1 (MQ=255)
                                                                                                                                  ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTa                                 <  4:538139/105‑1 (MQ=255)
                                                                                                                                  ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTa                                 >  3:538139/1‑105 (MQ=255)
                                                                                                                                        gCCGGATAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagt                                                        >  3:379063‑M1/1‑30 (MQ=255)
                                                                                                                                        gCCGGATAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagt                                                        <  4:379063‑M1/76‑47 (MQ=255)
                                                                                                                                         ccGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGc                                              <  3:402370/85‑1 (MQ=255)
                                                                                                                                         ccGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGc                                              >  4:402370/1‑85 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagttgttgattcccctggtgctagcgcaatgagatcacccccttccgggcgatgatg  <  1:89077‑M1/125‑101 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagttgttgattcccctggtgctagcgcaatgagatcacccccttccgggcgatgatg  >  2:89077‑M1/1‑25 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagttgttgattcccctggtgctagcgcaatg                            <  1:498515‑M1/99‑75 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagttgttgattcccctggtgctagcgcaatg                            >  2:498515‑M1/1‑25 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagttgttgattcccc                                            >  4:1084216‑M1/1‑25 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCatttaataaattacagccactctacccgcaacgacatctctgaagttgttgattcccc                                            <  3:1084216‑M1/83‑59 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATAtt                                   <  3:848075/92‑1 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATAtt                                   >  4:848075/1‑92 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAGGCGGCGAAGCtg               <  4:176072/112‑1 (MQ=255)
                                                                                                                                             aTAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAGGCGGCGAAGCtg               >  3:176072/1‑112 (MQ=255)
                                                                                                                                                aGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTc                                                          >  4:1052307/1‑66 (MQ=255)
                                                                                                                                                aGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTa                                 <  4:557640/91‑1 (MQ=255)
                                                                                                                                                aGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTa                                 >  3:557640/1‑91 (MQ=255)
                                                                                                                                                aGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGCTTGATTc                                                          <  3:1052307/66‑1 (MQ=255)
                                                                                                                                                |                                                                                                                         
CAAAAGGCGCACACTAAAGTCAGAGTGAGGGGGGGATGTTGGCGAATGTTGGCTTAGTGCCCAGGGTTCCCTCTCACCCTAACCCTCTCCCCGGTGGGGCGAGGGGACTGACCGAGCGCGTTGATAGCATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCACTCTTTCAGCAACATGGTTAGCGGAGGCCAAGATGTTTGATTCACTGGCAAAAGCCGGAAAATATTTAGGTCAGGCGGCGAAGCTGATGATTGGTATGC  >  NC_000913/631983‑632248

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: