Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	281,599	C→T	G129S (GGC→AGC)	yagA ←	CP4‑6 prophage; putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	281,599	0	C	T	92.7%	195.4 / 4.2	68	G129S (GGC→AGC)	yagA	CP4‑6 prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (1/4);  new base T (25/38);  total (26/42)
Fisher's exact test for biased strand distribution p-value = 6.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.14e-01

GGCAGCGTCCACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGCCAGCG  >  NC_000913/281503‑281692                                                                                                 |                                                                                              ggCAGCGTCCACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCgg                                                                                            <  2:121766/100‑1 (MQ=255) ggCAGCGTCCACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCgg                                                                                            >  2:1034988/1‑100 (MQ=255) ggCAGCGTCCACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCgg                                                                                            <  1:1716548/100‑1 (MQ=255)  gCAGCGTCCACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGt                                                                                           >  1:2170531/1‑100 (MQ=255)         ccACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAgcgc                                                                                    >  2:1124054/1‑100 (MQ=255)         caaCCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAgcgc                                                                                    >  2:1502078/3‑100 (MQ=255)          cACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGcc                                                                                   <  1:996777/100‑1 (MQ=255)              gCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGgc                                                                               >  1:341743/1‑100 (MQ=255)                     ccgatctGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGc                                                                        <  1:969653/94‑1 (MQ=255)                          gTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATgg                                                                   <  2:303153/100‑1 (MQ=255)                            ggCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGcagatcgg                                                                 >  2:969654/1‑93 (MQ=255)                              cccTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCggg                                                               <  1:827467/100‑1 (MQ=255)                              cccTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCggg                                                               <  2:485991/100‑1 (MQ=255)                               ccTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGCAGCGCCCGGCCGCAGGCCATGgcgcgc                                                              >  1:2164460/1‑100 (MQ=255)                               ccTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGc                                                              <  1:1753214/100‑1 (MQ=255)                                   aaaaTCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATc                                                          <  1:128835/100‑1 (MQ=255)                                    aaaTCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCa                                                         <  1:866601/100‑1 (MQ=255)                                     aaTCCATCTGCCGGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAg                                                        >  2:1467156/1‑100 (MQ=255)                                     aaTCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAg                                                        >  2:922278/1‑100 (MQ=255)                                      aTCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAgg                                                       <  2:1770244/100‑1 (MQ=255)                                        ccATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGCACCGGCCCGTGTCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAg                                                        <  1:1451743/97‑1 (MQ=255)                                          aTCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTAt                                                   <  2:247869/100‑1 (MQ=255)                                          aTCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTAt                                                   <  1:847547/100‑1 (MQ=255)                                          aTCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTAt                                                   >  1:1720693/1‑100 (MQ=255)                                           tCTGCCTGAGGCGGTTCGGCGCGTCGTGTTCGATCCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATg                                                  <  1:181083/100‑1 (MQ=255)                                            cTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATgg                                                 <  1:1312385/100‑1 (MQ=255)                                             tGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGa                                                >  1:1356515/1‑100 (MQ=255)                                              gCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCATGCCATGGCGGGCCATCAGGTTATGGAc                                               >  1:2046386/1‑100 (MQ=255)                                              gCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGAc                                               <  1:1685850/100‑1 (MQ=255)                                                cAGAGGCGGTTGGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACg                                              <  1:793850/99‑1 (MQ=255)                                                cAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACgg                                             <  2:1940788/100‑1 (MQ=255)                                                cAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACgg                                             >  1:1223153/1‑100 (MQ=255)                                                 agagGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGt                                            >  2:1691880/1‑100 (MQ=255)                                                   agGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGc                                          <  1:1124053/100‑1 (MQ=255)                                                    ggCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCt                                         >  2:1035962/1‑100 (MQ=255)                                                    ggCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCt                                         <  1:922277/100‑1 (MQ=255)                                                       ggTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGaa                                      <  1:1034987/100‑1 (MQ=255)                                                       ggTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGaa                                      <  2:532871/100‑1 (MQ=255)                                                       ggTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGaa                                      >  2:339170/1‑100 (MQ=255)                                                          tCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGc                                   <  1:2143420/100‑1 (MQ=255)                                                          tCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGc                                   <  2:2042360/100‑1 (MQ=255)                                                           cGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGACGTGCCATCAGGTTATGGACGGTGCTGAAGGCg                                  <  1:1467149/100‑1 (MQ=255)                                                            ggCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCgg                                 >  2:634859/1‑100 (MQ=255)                                                             gcgcGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCggg                                <  1:1818822/100‑1 (MQ=255)                                                             gcgcGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCggg                                <  2:1402389/100‑1 (MQ=255)                                                             gcgcGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCggg                                <  1:346715/100‑1 (MQ=255)                                                               gcgTCGTGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCa                              <  2:2019965/100‑1 (MQ=255)                                                                 gtcgtGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATg                            <  2:706939/100‑1 (MQ=255)                                                                  tcgtGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATgg                           <  2:1081694/100‑1 (MQ=255)                                                                  tcgtGTTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATgg                           <  1:307421/100‑1 (MQ=255)                                                                    gtgtTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGgtg                         <  2:2170543/100‑1 (MQ=255)                                                                    gtgtTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGgtg                         >  1:444860/1‑100 (MQ=255)                                                                    gtgtTCGAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGgtg                         >  1:972661/1‑100 (MQ=255)                                                                          gAACCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGcccc                   <  2:1720702/100‑1 (MQ=255)                                                                           aaCCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCt                  >  2:2124476/1‑100 (MQ=255)                                                                           aaCCGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCt                  >  2:2124756/1‑100 (MQ=255)                                                                             ccGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTgg                <  2:1243290/100‑1 (MQ=255)                                                                             ccGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTgg                <  2:2049189/100‑1 (MQ=255)                                                                             ccGGCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTgg                >  2:1684390/1‑100 (MQ=255)                                                                                gCCCGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTcc             >  1:399589/1‑100 (MQ=255)                                                                                  ccGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTc           <  1:307293/100‑1 (MQ=255)                                                                                   cggggCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCg          <  1:2160301/97‑1 (MQ=255)                                                                                   cGTGGCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTCCCCCTGGTCCtag          <  2:1497004/100‑3 (MQ=255)                                                                                      ggCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGc       >  1:766233/1‑100 (MQ=255)                                                                                       gCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGcc      >  2:488531/1‑100 (MQ=255)                                                                                       gCGGGAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGACGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGcc      <  2:1300150/100‑1 (MQ=255)                                                                                          ggAATGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGCCAgc   <  1:1791941/100‑1 (MQ=255)                                                                                           naaTGCTCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGCCAgcg  >  2:691364/2‑100 (MQ=255)                                                                                                 |                                                                                              GGCAGCGTCCACCGCCAAAAGGAAAGTGGCCCTTAAAATCCATCTGCCAGAGGCGGTTCGGCGCGTCGTGTTCGAACCGGCCCGTGGCGGGAATGCCCGGTGAAGCGCCCGGCAGCAGGCCATGGCGGGCCATCAGGTTATGGACGGTGCTGAAGGCGGGCATGGTGTGCCCCTGGTCCTCGAGCCAGCG  >  NC_000913/281503‑281692

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑