Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,864,099	0	C	A	43.4%	73.9 / 22.1	53	R67R (CGC→CGA)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (21/9);  new base A (0/23);  total (21/32)
Fisher's exact test for biased strand distribution p-value = 5.73e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

TAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATC  >  NC_000913/3863960‑3864243                                                                                                                                            |                                                                                                                                                 tAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACt                                                                                                                                       >  1:512938/1‑151 (MQ=255)  aaaCAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACt                                                                                                                                       <  2:407231/150‑1 (MQ=255)     cAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCAt                                                                                                                                   >  1:195802/1‑151 (MQ=255)      aGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAATAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTAcgacat                                                                                                                                   <  2:704035/150‑6 (MQ=255)        ccTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCa                                                                                                                                 >  2:990840/1‑150 (MQ=255)                      aaaaaaaGCGGGGGGAGGATTTTGGGGTATCGCGGATGACCATCCTTAAAGCCTTTGCCCTGCGGTTAGCGTGGGGGCTGGTGGTCCGCCCCCCCGGTAGTGTCACTTCCCGGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTg                                                                                                                    <  2:675207/149‑1 (MQ=255)                       aaaaaaGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGAcc                                                                                                                 >  2:914629/1‑151 (MQ=255)                             gCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtg                                                                                                           >  1:665984/1‑151 (MQ=255)                                gggggAAGAGTGTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCGCGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtggtg                                                                                                        <  1:664675/148‑1 (MQ=255)                                    gAAGAGTTTGCGGTACCGGGGATGACCATCCGTAAACCCTTTGACCGGCTGGTAGCGGGGGGGCGGTTGTTCCGCCGCCCCGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAg                                                                                                     <  1:537815/150‑1 (MQ=255)                                          tttGCGGTACCGCGGATAACCTCCCGTAAGGCCTTTGCCTGGTTGGGGGGGGGGGGGTTGGTGGCCCCCCCCCACGGTAGTGGCCCTTACCGGGTGCGAAAATATGTCCTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGa                                                                                                      <  2:741299/143‑1 (MQ=255)                                               ggTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACgg                                                                                         >  1:735999/1‑151 (MQ=255)                                               agTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACgg                                                                                         >  1:954966/2‑151 (MQ=255)                                                 tacggcgGATGACCATCCGTAAAGCCTTGGACCTGCTGGTAGGGGGGGGGTTGGTGTTCCGCCGCCACGGTGGTGGCCCTTACCGGGTGGGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACgg                                                                                         <  2:325601/145‑1 (MQ=255)                                                 tATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGc                                                                                        >  2:749787/1‑150 (MQ=255)                                                  aTCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGc                                                                                        >  1:853283/1‑149 (MQ=255)                                                    cgcgGATGACCACCCGTAAAGCCTTTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAg                                                                                      <  1:105748/149‑1 (MQ=255)                                                     gcgGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCGGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAggg                                                                                    <  1:597722/150‑1 (MQ=255)                                                       ggATGCCCACCCGTAAAGCCATTGCCCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaa                                                                                  <  1:32081/150‑1 (MQ=255)                                                       ggATGCCCACCCAAAAAGCTTTTGCCCTGCGGGTAGCGGGGGGGCGGGGGGCCCGCCGCCACGGTAGTGGCACTTACCTGGGGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGa                                                                                   <  2:980788/149‑1 (MQ=255)                                                        gttgcccATCTGTAAAGCCATTGCCCTGCTGGTAGTGGGGGGGTTGGTGGCCCGCCGCCAGGTTGGTGGCACTTCCCTGGTGCGCAAAGATGTACTGCACCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAggg                                                                                    <  1:607546/142‑1 (MQ=255)                                                         aTGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaaa                                                                                >  1:893964/1‑150 (MQ=255)                                                            accaccCGAAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGCCCGCCGCCACGGTAGTGGCACTTCCCGGGTGCGAAAAGATGTACTGCAAAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaaaa                                                                               <  1:641649/148‑1 (MQ=255)                                                              cacccGTAAACCCTTTGCCCTGCGGGTGGGGTGGGGGTTGGTGGTCCGCCGCCAGGGTAGTGGCCCTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTc                                                                          <  2:954880/148‑1 (MQ=255)                                                                tCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAc                                                                        >  1:73321/1‑151 (MQ=255)                                                                 ccGTAAAGCCTTTGCCCTGCTGGTGGGGTGGGGGCGGGTGGTCCGCCGCCACGGTGGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAc                                                                        <  2:583229/150‑1 (MQ=255)                                                                 ccGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAcc                                                                       >  1:423040/1‑151 (MQ=255)                                                                  cgaaaaGCCATGGCCCTGTTGGTAGGGTGGGGGCTGGTGGGCCGCGCCCACGGTGGTGCCACTTACCTGGTGCACAAAAATGTACTGCACCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAcca                                                                      <  1:306286/148‑1 (MQ=255)                                                                   gTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAcc                                                                       >  2:90126/1‑149 (MQ=255)                                                                     aaaGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcc                                                                   >  2:549717/1‑151 (MQ=255)                                                                      aaGCCTTTGCCCTGCTGGTGGCGTGGGGGCGGGTGGTCCCCCCCCACGGTAGGGGCCCTTCCCTGGTGCGCAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcca                                                                  <  2:665913/151‑1 (MQ=255)                                                                      aaGCCATTGCCCTGCTGGTAGCGTGGGGGCTGGTGGCCCGCCGCCACGGTAGGGGCACTTCCCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcca                                                                  <  1:846233/151‑1 (MQ=255)                                                                         ccttgacccggttgGTAGCGTGGGGGCGGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATTTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGt                                                               <  1:506544/139‑1 (MQ=255)                                                                         ccATTGCCCTGCTGGTGGGGGGGGGGCGGGTGGCCCGCCGCCGGGGTAGGGGCCTTTCCCGGGGGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAgg                                                                <  2:195779/150‑1 (MQ=255)                                                                         ccATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagccag                                                                 >  1:301393/1‑149 (MQ=255)                                                                              gcccTGCGGGTGGGGGGGGGGGGGGTGGCCCGCCGCCAGGGTAGTGGCCCTTACCGGGGGCGAAAAGATGTACTGCAACAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCt                                                            <  2:334497/147‑1 (MQ=255)                                                                              gACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTg                                                           >  1:304448/1‑150 (MQ=255)                                                                                       gtggggTGGGGGGTGGTGCCCCGCCCCCAGGGTGGTGGCTCTTTCCGGGGGCGAAAATTTGTACTCCAACAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGAttttt                                                     <  2:936833/142‑1 (MQ=255)                                                                                        tAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGaaa                                                 >  2:753608/1‑150 (MQ=255)                                                                                         aGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATc                                               >  1:106207/1‑151 (MQ=255)                                                                                            gggggggTTGGTGGGCCGCCCCCGCGGTAGGGGCACTTCCCTGGTCCGCAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATc                                               <  1:605453/146‑1 (MQ=255)                                                                                             tGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGc                                           >  1:116975/1‑151 (MQ=255)                                                                                              gggggTGGGTGGCCCCCCGCCACGGTAGGGGCACTTCCCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATg                                            <  2:156969/149‑1 (MQ=255)                                                                                               ggggCTGGTGGTCCGCCGCCACGGTAGTGGCCCTTCCCTGGTGCGAAAAGATGTACGGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCt                                         <  1:867200/151‑1 (MQ=255)                                                                                                              cccccACGGTAGTGGCACTTACCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCAtt                          <  2:303775/148‑1 (MQ=255)                                                                                                                  cgcGGTAGTGGCTTTTCCCGGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgcca                      <  2:356058/149‑1 (MQ=255)                                                                                                                   aCGGTAGTGGCACTTCCCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccag                     <  1:534575/151‑1 (MQ=255)                                                                                                                     ggtggtGCCACTTACCTGGTGGGAAAGGATGTACTGCATAAACCCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccagcc                   <  2:681610/151‑1 (MQ=255)                                                                                                                                   ccgggTGCGCAAAGATTTACGGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTc       <  2:981367/146‑1 (MQ=255)                                                                                                                                   ccTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCa      >  2:760454/1‑150 (MQ=255)                                                                                                                                    cTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCaa     >  2:278394/1‑150 (MQ=255)                                                                                                                                      ggTGCGAAAAGATGTCGGGTACCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGAtt        <  2:95489/145‑1 (MQ=255)                                                                                                                                      ggTGCGAAAAGATGTACTGCACAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATc  <  2:223123/151‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                 TAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATC  >  NC_000913/3863960‑3864243

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑