Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,864,099	0	C	A	43.1%	71.4 / 20.0	51	R67R (CGC→CGA)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (20/9);  new base A (0/22);  total (20/31)
Fisher's exact test for biased strand distribution p-value = 1.68e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

AGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCA  >  NC_000913/3863949‑3864244                                                                                                                                                       |                                                                                                                                                  aGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTgcgc                                                                                                                                                   >  1:786613/1‑151 (MQ=255) aGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTgcgc                                                                                                                                                   >  2:802392/1‑151 (MQ=255)  gATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCa                                                                                                                                                  <  1:490502/151‑1 (MQ=255)     ttCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCaa                                                                                                                                                 >  2:349848/1‑149 (MQ=255)      tCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAg                                                                                                                                               <  1:178652/150‑1 (MQ=255)          gCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGt                                                                                                                                           >  2:834449/1‑150 (MQ=255)           cTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTa                                                                                                                                          >  2:71422/1‑150 (MQ=255)                 aGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATc                                                                                                                                   >  2:582627/1‑151 (MQ=255)                    cttcttCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCaa                                                                                                                                 >  1:237601/1‑150 (MQ=255)                         tcCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAAcc                                                                                                                              <  2:442235/148‑1 (MQ=255)                           ccGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAg                                                                                                                         <  1:154646/151‑1 (MQ=255)                             ggTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTc                                                                                                                       >  1:313581/1‑151 (MQ=255)                                  aaaaaaGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACAGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGAcc                                                                                                                  >  2:186932/1‑151 (MQ=255)                                    aaaaGCTGGCGGAAGAGTTGGCGGTTTCGCGGATGCCCATCCGTAAAGCCATTGCCCTGCTGGTAGCGTGGGGGCTGGTGGCCCGCCGCCACGGTGGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCgg                                                                                                                <  1:26946/151‑1 (MQ=255)                                     aaaGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCggg                                                                                                               >  1:257205/1‑151 (MQ=255)                                      aaGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGc                                                                                                              >  2:114070/1‑151 (MQ=255)                                        gCTGGCGGAAGAGTTTGCGGTATCGCGGATGCCCATCCGTAAAGCCATTGCCCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCt                                                                                                             <  1:762048/150‑1 (MQ=255)                                          tGGGGGAAGAGTTTGGGGTAGCGCGGATGCCCATCCGTAAAGCCATTGACCTGCTGGTAGGGGGGGGGCTGGGGGTCCGCCCCCACGGTGGTGGCACTTACCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtg                                                                                                            <  2:76142/149‑1 (MQ=255)                                            gCGGAAGTGTTTGCGTTCTCGCGGATGACCATCCGAAAAGCCATGGACCTGCTGGTGGGGGGGGGGCTGGTGGTCCGCCGCCACGGTGGTGGCCCTTACCGGGTGCGAAAAGATGTACGGCATCAAACCGCCAGTCTGACCGGGCtggt                                                                                                          <  2:221785/149‑1 (MQ=255)                                                        gCGGTATCGGGGATGACCATCCGGAAAGCCATGGACTTGCGGGGAGGGGGGGGGCGGGGGGTCCCGCCCCACGGTAGGGGCGTTTCCAGGGGGCGCAAAGATGTATTGAATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTaaaa                                                                                             <  2:726289/150‑1 (MQ=255)                                                         cGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACg                                                                                           >  1:346802/1‑151 (MQ=255)                                                           gTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGc                                                                                         >  2:675163/1‑151 (MQ=255)                                                                    aTGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaaa                                                                                 >  1:321243/1‑150 (MQ=255)                                                                      gACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACg                                                                              >  2:551906/1‑151 (MQ=255)                                                                        ccATCCGAAAAGCCATTGCCCTGCTGGTAGCGGGGGGGCGGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGt                                                                            <  1:54804/151‑1 (MQ=255)                                                                           tCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAc                                                                         >  2:455712/1‑151 (MQ=255)                                                                             cGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAcca                                                                       <  1:171861/151‑1 (MQ=255)                                                                                  aGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagccat                                                                  >  1:565490/1‑150 (MQ=255)                                                                                    cctttGCCCTGCTGGTGGCGGGGGGGTGGGGGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGt                                                                <  1:140035/148‑1 (MQ=255)                                                                                    ccATTGACCTGCTGGTGGCGTGGGGGCTGGTGGCCCGCCGCCACGGTAGTGGCACTTACCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAgg                                                                 <  1:544576/150‑1 (MQ=255)                                                                                       ttGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCt                                                             >  2:454085/1‑151 (MQ=255)                                                                                           ccTGCTGGGAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGGGCTGAtt                                                         >  2:654835/1‑151 (MQ=255)                                                                                                 ggTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGaa                                                   <  1:81170/151‑1 (MQ=255)                                                                                                 ggTAGCGTGGGGGCTGGTGGTCCGCCCCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGAttttt                                                      <  1:117538/148‑1 (MQ=255)                                                                                                   tAGCGGGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGaaa                                                  <  1:361287/150‑1 (MQ=255)                                                                                                    aGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATc                                                >  2:352583/1‑151 (MQ=255)                                                                                                     gggggggggCTGGTGGTCCGCCGCCACGGTAGTGGCCCTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATc                                                <  1:728903/146‑1 (MQ=255)                                                                                                          ggggCTGGTGTTCCGCCGCCACGGTAGTGGCACTTCCCTGGGGCGCAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCt                                          <  1:476534/151‑1 (MQ=255)                                                                                                                   ggtCCGCCGCCAGGGTGGTGCCACTTCCCTGGTGCGAAAAGATGTCCTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTcc                                  <  1:342885/150‑1 (MQ=255)                                                                                                                   ggtCCGCCGCCACGGTAGTGGCACTTCCCTGGGGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCg                                 <  1:87552/151‑1 (MQ=255)                                                                                                                            ccccGGTAGTGGCCCTTCCCTGGTGCGAAAAGATGTCCTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTg                          <  1:333650/146‑1 (MQ=255)                                                                                                                             cACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgcca                       <  1:447097/151‑1 (MQ=255)                                                                                                                                ggTAGTGGCCCTTCCCTGGTGCGAAAAGATGTACGCCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgcca                       <  1:389410/148‑1 (MQ=255)                                                                                                                                ggTAGTGGCACTTCCCGGGTGCGAAAAGTTGTCCTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgcca                       <  1:260252/148‑1 (MQ=255)                                                                                                                                 gTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccagcca                   <  1:186967/151‑1 (MQ=255)                                                                                                                                      ggCACTTACCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTAc              <  1:788027/151‑1 (MQ=255)                                                                                                                                         ccTTCCCTGGTGCGAAAAGATGTACGCCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACgg            <  2:676482/149‑1 (MQ=255)                                                                                                                                          cTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGAt          >  1:89072/1‑151 (MQ=255)                                                                                                                                           ttACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGAtt         >  1:287229/1‑151 (MQ=255)                                                                                                                                              ccTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTc        <  1:552045/149‑1 (MQ=255)                                                                                                                                                 ggTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATc   <  1:774405/151‑1 (MQ=255)                                                                                                                                                 ggTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATc   <  1:63113/151‑1 (MQ=255)                                                                                                                                                  gTGCGAAAAGATGTACTGCAGCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCa  <  2:415022/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                  AGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCA  >  NC_000913/3863949‑3864244

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑