Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,042,993	0	C	T	42.0%	62.3 / 19.5	51	F193F (TTC→TTT)	srkA	Cpx stress response Thr/Ser protein kinase; MazF antagonist protein
Reads supporting (aligned to +/- strand):  ref base C (9/20);  new base T (21/0);  total (31/20)
Fisher's exact test for biased strand distribution p-value = 2.24e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGACCATCGGTTTGAACGAATATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGAGCAGC  >  NC_000913/4042848‑4043138                                                                                                                                                   |                                                                                                                                                   cGACCATCGGTTTGAACGAATATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGAATTTAcc                                                                                                                                                 >  2:796082/1‑149 (MQ=255)     cATCGGTTTGAACGAATATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCt                                                                                                                                            >  1:781519/1‑150 (MQ=255)       tCGGTTTGAACGAATATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGtt                                                                                                                                              >  1:730103/1‑146 (MQ=255)            ttGAACGAATATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GGAGGGTTTAGCCTTCCGCGGGTAc                                                                                                                                    >  1:227302/1‑151 (MQ=255)             tGAACGAATATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTAc                                                                                                                                    >  1:1174783/1‑150 (MQ=255)                   aaTATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGgaga                                                                                                                             <  2:534465/151‑1 (MQ=255)                         tcATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTGCGGCTACATGGAGACTGcc                                                                                                                        >  1:1113751/1‑150 (MQ=255)                                 ccACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GGAGATTTTACCGTTCTGCGGCTACATGGGGACTGCCCCGCCggg                                                                                                                >  2:674665/1‑150 (MQ=255)                                     gCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAatat                                                                                                           <  1:1194323/151‑1 (MQ=255)                                     gCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGAATTTACCGTTCTGCGGCTACATGGGGACTGCCCCGCCggg                                                                                                                >  2:205504/1‑146 (MQ=255)                                      cAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTGCGGCTACATGGGGACTGCCACGCCGGGGATAtt                                                                                                          >  1:1326224/1‑151 (MQ=255)                                      cAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGGTCTGCGGCTACATGGAGACTGCCACGCCGGGGATAtt                                                                                                          >  1:191626/1‑151 (MQ=255)                                          cTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GGAGATTTTACCGTTCTGCGGCTACATGGGGACCGCCACGCCGGGAATAtt                                                                                                          >  1:584899/1‑147 (MQ=255)                                                   gACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATg                                                                                             <  1:812864/151‑1 (MQ=255)                                                           acTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GGAGAATTTTCCGTTTTGCGGCGACAAGGGGGGCGCCACGCCGGGGAGATTCTCTGGCGCGCTggggccat                                                                                      >  2:1171214/1‑144 (MQ=255)                                                              gATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAAtgtt                                                                                  <  2:577163/150‑1 (MQ=255)                                                                  ccTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTGCGGCTACATGGGGACTGCCCCGCCGGGGATATTTTCTGGCGCGATGGT‑CCAAagtttgtt                                                                              >  1:713281/1‑150 (MQ=255)                                                                   cTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGGTGAGGGTTTACCAGTTC‑GTGGCTCAGTGGAGAGTGGCACCCCGGGGCTATTGTCTGGGCCGGTGGTACCAAcgttgctgg                                                                             >  1:816046/1‑146 (MQ=255)                                                                    ttCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTGGGGCTACCTGGAGGCTGCCACGCCCGGAATATTTTCTGGCGCGATGGT‑CCCATTTTTGTTTAt                                                                           >  1:458230/1‑151 (MQ=255)                                                                         ggTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GCAGATTTCACCGCTCTTCGGCCACCTCGAGACTGCCCCGCCGGGGATATTTTCTGGTCCGGTGGG‑CCCATGTTTGGTGaac                                                                          >  1:1100640/1‑145 (MQ=255)                                                                         ggTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGGTCTGCGGCTACATGGGGACCGCCCCGCCGGGGATATTTTCTTGCGCGGTGGG‑TCCATGTTTGTTTAttt                                                                         >  1:1016316/1‑146 (MQ=255)                                                                                aGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTTGGGCCGCCTGGGGGATGCCCCGCCGGGGAAATTTTCTTGCGCGAGGGG‑CCAAcgtttgttttacttggtg                                                                    >  2:20943/1‑136 (MQ=255)                                                                                   ggCATTCCTGAAAGCGACAGATGAGCTGATCGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGt                                                            <  1:755860/151‑1 (MQ=255)                                                                                      aTTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTGCGGGTACAAGGAGACTGCCACGCCGGGGATATTCTCTGGCGCGATGGT‑CCCATGTTTGTTGATCTGGGTGATGCACGTAAt                                                         >  1:519438/1‑151 (MQ=255)                                                                                      aTTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTGCGGCTACATGGAGACTGCCACGCCCGGGATATTCTTTGGCGCGGTGGG‑CCCATGTTTGTTGATCTGGATGATGCACGGaa                                                          >  1:79478/1‑150 (MQ=255)                                                                                         ccTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GGAGAATTTACCGTTTTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGGTCTGGAGGATGCACGTAATgg                                                       >  2:810828/1‑150 (MQ=255)                                                                                              aaGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGGTACATTGAGACTGGCACCCCGGGGAAATTTTCTGGGGCGGTGGT‑CCAAAATTTGTTGGTTTGGGTGATGCACGTAATGGTCCAg                                                  >  1:193217/1‑150 (MQ=255)                                                                                               aGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGcc                                                >  1:55927/1‑151 (MQ=255)                                                                                               aGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGcc                                                <  1:513777/151‑1 (MQ=255)                                                                                               aGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGcc                                                <  2:1302887/151‑1 (MQ=255)                                                                                                   aCAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGGTTTGCGGCGACAAGGAGACTGCCACGCCGGGGATATTTTCTTGCGCGATGGT‑CCAATGGTTGTTGGTCTGGATGATGCACGTAAAGGTTCAGCCggt                                             >  2:946152/1‑148 (MQ=255)                                                                                                     aGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGAATTTACCGGTCTGCGGCCACAAGGGGACTGCCCCCCCGGGGATATTTTCTGGCGCGGGGGT‑CCAATGGTTGTTGATCTGGATGGTGCACGTAATGGGCCGGCCGtt                                             >  2:146068/1‑148 (MQ=255)                                                                                                      gATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAAATTTTACCGGTCTGCGGCTACATGGGGACTGCCACGCCGGGAATATTTTCTGGCGCGGTGGG‑CCAATGTTTTTTGATCTGGATGATGCACGGAATGGTCCAGCCGTTTAgg                                         >  1:402770/1‑151 (MQ=255)                                                                                                              gATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTtgtg                                  <  2:822424/150‑1 (MQ=255)                                                                                                                ttGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTTACCGGTCTGCGGCTACATGGAGACTGCCCCGCCGGGGATATTTTCTGGCGCGATGGG‑CCAATGTTTGTTGATCTGGGTGATGGACGGAATGGTCCAGCCGGTCAGGAttt                                     >  1:1272772/1‑145 (MQ=255)                                                                                                                 tGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGAt                               <  1:205511/150‑1 (MQ=255)                                                                                                                   ccgccgTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGtt                            <  1:693820/151‑1 (MQ=255)                                                                                                                     gccgTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGc                          <  2:446554/151‑1 (MQ=255)                                                                                                                            cAGCACACTGGCGG‑GAAGATTTTACCGCTCTGCGGCTACAAGGAGAATGGCACGCCGGGGATATTCTCTGGCGCGCTGGT‑CCAATGTTTTTTGATCTGGGTGATGCACGTCATGGTCCAGCCCTCCAGGATTTGTGGGTGTTGCTCAATgg                   >  2:651273/1‑151 (MQ=255)                                                                                                                              gCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCg                 <  2:914816/151‑1 (MQ=255)                                                                                                                                      gCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGcc         <  2:603967/151‑1 (MQ=255)                                                                                                                                       cGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCg        <  2:191620/151‑1 (MQ=255)                                                                                                                                       cGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCg        <  2:587517/151‑1 (MQ=255)                                                                                                                                        gg‑gAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCg        >  1:1153828/1‑150 (MQ=255)                                                                                                                                         g‑gAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCg        >  2:1069226/1‑149 (MQ=255)                                                                                                                                         g‑gAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGag      <  1:46234/151‑1 (MQ=255)                                                                                                                                           gAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGagc     <  2:730084/151‑1 (MQ=255)                                                                                                                                            aaGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGagca    <  2:781494/151‑1 (MQ=255)                                                                                                                                              gATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGagcagc  <  2:1017688/151‑1 (MQ=255)                                                                                                                                              gATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGagcagc  <  2:584884/151‑1 (MQ=255)                                                                                                                                              gATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGagcag   >  2:623214/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                   CGACCATCGGTTTGAACGAATATCTCATTGAGCCACGCAAGCTGTTTGAGGACGCTACACTGATACCTTCCGGGTTGAAAGCGGCATTCCTGAAAGCGACAGATGAGCTGATTGCCGCCGTTACAGCACACTGGCGG‑GAAGATTTCACCGTTCTGCGGCTACATGGAGACTGCCACGCCGGGAATATTCTCTGGCGCGATGGT‑CCAATGTTTGTTGATCTGGATGATGCACGTAATGGTCCAGCCGTTCAGGATTTGTGGATGTTGCTCAATGGCGATAAAGCCGAGCAGC  >  NC_000913/4042848‑4043138

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑