Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,880,549	T→C	100%	T71A (ACC→GCC)	leuE ←	leucine efflux protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,880,549	0	T	C	99.1%	244.5 / ‑6.1	75	T71A (ACC→GCC)	leuE	leucine efflux protein
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (39/34);  total (41/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTTACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCATACC  >  NC_000913/1880452‑1880645                                                                                                  |                                                                                                 tttttACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGAGGCCt                                                                                                >  2:3009431/1‑100 (MQ=255)  ttttACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAGTATCGGGGTGGCCtt                                                                                               >  1:3004784/1‑100 (MQ=255)   tttACCCTTCAGGGTCGCGTGAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCtta                                                                                              >  2:1846927/1‑100 (MQ=255)      aCCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaatt                                                                                           <  2:1350470/100‑1 (MQ=255)       cccTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCttaatta                                                                                          >  2:1539495/1‑100 (MQ=255)         cTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTtaattaat                                                                                        <  1:1797448/100‑1 (MQ=255)           tCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGAGTGGCCTTAATTAATGt                                                                                      >  2:126706/1‑100 (MQ=255)            cAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTc                                                                                     <  2:1630012/100‑1 (MQ=255)             agagTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCg                                                                                    <  1:2175600/97‑1 (MQ=255)              gggTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGc                                                                                   >  1:1790123/1‑100 (MQ=255)              gggTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGc                                                                                   >  1:91509/1‑100 (MQ=255)                ntCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCa                                                                                 >  1:2290147/2‑100 (MQ=255)                    cgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTcc                                                                             >  2:646689/1‑100 (MQ=255)                    cgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTcc                                                                             <  1:185730/100‑1 (MQ=255)                    cgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTc                                                                              >  1:2945350/1‑99 (MQ=255)                    cgTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACACAACAAGATAACGTAAAATATTCAATAACACCGGGGTAGACTTAATTAATCTCGTCACTc                                                                              >  2:2005911/1‑99 (MQ=255)                       aaaGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGc                                                                          >  1:2543239/1‑100 (MQ=255)                       aaaGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGc                                                                          >  1:1995661/1‑100 (MQ=255)                       aaaGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGc                                                                          >  1:1867929/1‑100 (MQ=255)                              tttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGTGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGcc                                                                   <  1:2136739/100‑1 (MQ=255)                              tttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGcc                                                                   <  1:1859762/100‑1 (MQ=255)                               tttcTCCCCAGATAGAGCAAATAAAACACTCCAAGATAACGTACAATGTTGAATAATATCAGGGTGGCCGTAATTAATGTCGCCACTCCAGCCCATGcc                                                                   <  1:860328/96‑1 (MQ=255)                               ttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCa                                                                  <  1:1522161/100‑1 (MQ=255)                               ttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCa                                                                  <  1:2480272/100‑1 (MQ=255)                               ttACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGATGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCa                                                                  >  1:83591/1‑100 (MQ=255)                                  cTCCCCAGATAGAGCAAATAAATCGCACCAAGATAATGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGaa                                                               <  1:13670/100‑1 (MQ=255)                                    ccccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGATGGCCTTAATTAATGTCGCCACTCCAGCCCATGACAGAAAc                                                             >  1:2536648/1‑100 (MQ=255)                                     cccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACa                                                            <  2:77744/100‑1 (MQ=255)                                     cccAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACa                                                            <  1:1963936/100‑1 (MQ=255)                                       cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                          <  1:1222613/100‑1 (MQ=255)                                       cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATc                                                          <  2:1122916/100‑1 (MQ=255)                                       cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGAGCTGGCCATAATTAATGTCGCCACTACAGACAATACCCGaaaaa                                                            >  2:783848/1‑96 (MQ=255)                                       cAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAAAAATATCGGGGTGACCTTAATTAATATCACCACTCCAGCCCATGCCAGAAACa                                                            >  2:162157/1‑98 (MQ=255)                                             gagCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATAcc                                                    >  1:2236527/1‑100 (MQ=255)                                             gagCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAAtcc                                                     >  2:2240452/1‑97 (MQ=255)                                             gagCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATAcc                                                    >  2:505687/1‑100 (MQ=255)                                              agCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCg                                                   <  1:2186711/100‑1 (MQ=255)                                              agCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCg                                                   <  1:2175899/100‑1 (MQ=255)                                              aacAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCg                                                   <  2:2104521/98‑1 (MQ=255)                                               gCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAAGATCaa                                                        <  2:671240/94‑1 (MQ=255)                                                cAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGc                                                  >  2:2675609/1‑99 (MQ=255)                                                cAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCa                                                 >  1:2682709/1‑100 (MQ=255)                                                 aaaTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCAt                                                >  1:2426308/1‑100 (MQ=255)                                                 aaaTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCAt                                                >  1:924988/1‑100 (MQ=255)                                                 aaaTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATACCAGAAACATCAATACCGCAt                                                >  1:140475/1‑100 (MQ=255)                                                  aaTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATc                                               >  1:2183508/1‑100 (MQ=255)                                                   aTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCg                                              >  1:2404297/1‑100 (MQ=255)                                                   aTAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCg                                              <  1:2509317/100‑1 (MQ=255)                                                     aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                            >  1:447414/1‑100 (MQ=255)                                                     aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                            <  1:1948702/100‑1 (MQ=255)                                                     aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                            <  2:1694605/100‑1 (MQ=255)                                                     aaaaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGcc                                            <  2:1334518/100‑1 (MQ=255)                                                       aaCGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCa                                           >  2:2677721/1‑99 (MQ=255)                                                             ccAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataaata                                    >  2:1571212/1‑100 (MQ=255)                                                             ccAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataaata                                    <  2:2238568/100‑1 (MQ=255)                                                             ccAAGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCaataaat                                     <  2:1878909/99‑1 (MQ=255)                                                               aaGATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATaca                                  <  2:2543208/100‑1 (MQ=255)                                                                 gATAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACAcc                                <  2:1248968/100‑1 (MQ=255)                                                                   tAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGc                              <  2:2592220/100‑1 (MQ=255)                                                                   tAACGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGACAGAAACATCAATACCGCATCGCCAATAAATACACCGc                              >  1:975973/1‑100 (MQ=255)                                                                     aCGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCa                             >  1:1877766/1‑99 (MQ=255)                                                                      cGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCACAgg                           >  1:2266611/1‑100 (MQ=255)                                                                      cGTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCACAAACATCAATACCGCATCGCCAATAAATACACCGCa                             >  2:1428709/1‑98 (MQ=255)                                                                       gTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGc                          >  1:405147/1‑100 (MQ=255)                                                                       gTACAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGc                          >  1:2002180/1‑100 (MQ=255)                                                                          cAATGTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAAAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGc                       >  1:263415/1‑100 (MQ=255)                                                                              gTTGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGa                   <  1:2677753/100‑1 (MQ=255)                                                                                tGAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCTCAGGCCGCAAGATa                 <  2:107189/100‑1 (MQ=255)                                                                                 gAATAATATCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCTGAAACATCAATACCGCATCGCCAATAAATACCCCGCAGGCCGCAAGATaa                >  2:1932236/1‑100 (MQ=255)                                                                                     aataTCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACAGAAGGCCGCAAGATAAcccc            >  1:2841283/1‑98 (MQ=255)                                                                                      atatCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGcn           <  2:2290121/100‑2 (MQ=255)                                                                                      atatCGGGGTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGcc           >  1:741293/1‑100 (MQ=255)                                                                                           ggggTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCa      <  2:59312/100‑1 (MQ=255)                                                                                           ggggTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCa      <  1:1928430/100‑1 (MQ=255)                                                                                            gggTGGCCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCAt     <  2:2976658/100‑1 (MQ=255)                                                                                             ggtggcCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTc       <  2:372384/97‑1 (MQ=255)                                                                                              gtggcCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCATa    <  2:741289/99‑1 (MQ=255)                                                                                               tggcCTTTATTAATGTCGCCACTCCAGCCCTTGCCAGAATCATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCATAcc  <  1:965836/100‑1 (MQ=255)                                                                                                  |                                                                                                 TTTTTACCCTTCAGGGTCGCGTAAAGAATTTTACTCCCCAGATAGAGCAAATAAAACGCACCAAGATAACGTACAATGTTGAATAATATCGGGGTGGTCTTAATTAATGTCGCCACTCCAGCCCATGCCAGAAACATCAATACCGCATCGCCAATAAATACACCGCAGGCCGCAAGATAACCGCCTTTCATACC  >  NC_000913/1880452‑1880645

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: ‑