Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,645,034	0	A	C	21.1%	97.8 / 13.3	52	intergenic (‑132/+85)	rem/hokD	Qin prophage; protein Rem/Qin prophage; toxic protein HokD
Reads supporting (aligned to +/- strand):  ref base A (30/11);  new base C (0/11);  total (30/22)
Fisher's exact test for biased strand distribution p-value = 1.17e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01
Rejected as consensus: Frequency below/above cutoff threshold.

TTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTT  >  NC_000913/1644895‑1645170                                                                                                                                            |                                                                                                                                          ttCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATaaaaacaaaaa                                                                                                                                           >  2:186904/1‑140 (MQ=255)      catcaGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑Cccgc                                                                                                                                     >  1:1119655/1‑140 (MQ=255)           gAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAg                                                                                                                                <  1:186904/140‑1 (MQ=255)                   ccGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCGGCGGAAGCGGGTTaa                                                                                                                        >  1:1072503/1‑140 (MQ=255)                         aaTTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCgg                                                                                                                  <  2:1119655/140‑1 (MQ=255)                                   ccccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAg                                                                                                        >  2:483940/1‑140 (MQ=255)                                    cccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCggg                                                                                                                 >  2:1172463/1‑130 (MQ=255)                                    cccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCggg                                                                                                                 <  1:1172463/130‑1 (MQ=255)                                    cccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAgg                                                                                                       <  1:891370/140‑1 (MQ=255)                                    cccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAgg                                                                                                       >  1:1247746/1‑140 (MQ=255)                                     ccTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGa                                                                                                      >  2:800238/1‑140 (MQ=255)                                         tAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGAtgcc                                                                                                  >  1:314477/1‑140 (MQ=255)                                         tAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGAtgcc                                                                                                  <  1:349459/140‑1 (MQ=255)                                            gggACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCggg                                                                                                                 >  2:476043/1‑122 (MQ=255)                                            gggACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCggg                                                                                                                 <  1:476043/122‑1 (MQ=255)                                            gggACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGAtgcctgc                                                                                               >  1:288410/1‑140 (MQ=255)                                                ccATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCcaca                                                                                           >  2:1230040/1‑140 (MQ=255)                                                                 gcgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGa                                                                          >  1:603518/1‑140 (MQ=255)                                                                 gcgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGa                                                                          >  1:126451/1‑140 (MQ=255)                                                                  cgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGAt                                                                         <  1:1019239/140‑1 (MQ=255)                                                                  cgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGTGCTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGAt                                                                         >  2:837369/1‑140 (MQ=255)                                                                  cgcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGGGGATGCCTGCCACATCAGAGGTGGCGAGGGAt                                                                         >  1:229922/1‑140 (MQ=255)                                                                   gcgcTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGAtt                                                                        >  1:1039499/1‑140 (MQ=255)                                                                       tACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTtctc                                                                    >  1:833296/1‑140 (MQ=255)                                                                          ttAAGTTTTTTTGTTTTTATCCGGGCCCCGCCAAGACCTTAAAAGGGGTTAAAAAAAAAAACAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTcccc                                                                 <  2:288410/140‑1 (MQ=255)                                                                            atgTATTTTTAATTCTATTCCGGCACCGCCAAAAACTTCAAGCGCGTTGAAAATAAAAAAAAAAC‑CCCCCCCAGGCGGGTTAACGGCGGGTGCATTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCccg                                                               <  2:1247746/138‑1 (MQ=255)                                                                             aGTTTTTTTGATTCTATCCCGGCCCCGTCCAGAACTTCAAACGCGTTAAAAAAAAAAAAAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCccgc                                                              <  2:126451/140‑1 (MQ=255)                                                                              ttATTTTGAATTCTATCCCGCCACCGCCAAGAA‑TTAAAACCGGGTGAAAAAAAAAAAAAAAACCCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCccgcc                                                             <  2:1230209/139‑1 (MQ=255)                                                                              gtttttttGATTCTATCCCGCCCCCGTCCAGACCTTAAACCGGGTTAAAAAAAAAAACAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCccgcc                                                             <  2:833296/137‑1 (MQ=255)                                                                                 tttttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCggg                                                          >  1:1135667/1‑140 (MQ=255)                                                                                 tttttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCggg                                                          >  2:154106/1‑140 (MQ=255)                                                                                 tttttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCggg                                                          >  2:691523/1‑140 (MQ=255)                                                                                 tttttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTAAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCggg                                                          <  1:691523/140‑1 (MQ=255)                                                                                   tttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGtc                                                        >  2:430654/1‑140 (MQ=255)                                                                                   tttGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGtc                                                        >  2:66536/1‑140 (MQ=255)                                                                                      gATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAACCAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTctct                                                     <  1:1169477/140‑1 (MQ=255)                                                                                               ccgcccccGCCCAGACCTTAAACCGCGTTAAAAAAAAAAAAAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCa                                            <  2:1171384/134‑1 (MQ=255)                                                                                               ccGGCCCCGCCAAAAACTTAAAACGCGTGAAAAAAAAAAAAAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCa                                            <  2:1039499/140‑1 (MQ=255)                                                                                               ccGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCa                                            <  1:800238/140‑1 (MQ=255)                                                                                                  gCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGt                                         >  2:35761/1‑140 (MQ=255)                                                                                                  gCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGt                                         >  1:301618/1‑140 (MQ=255)                                                                                                       gTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGGGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTa                                    >  1:240348/1‑140 (MQ=255)                                                                                                        tCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTaa                                   <  1:35761/140‑1 (MQ=255)                                                                                                        tCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTaa                                   >  2:522113/1‑140 (MQ=255)                                                                                                        tCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTaa                                   >  1:420699/1‑140 (MQ=255)                                                                                                                ttCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGaa                           >  2:1114067/1‑140 (MQ=255)                                                                                                                ttCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTAGTAAGCTGTGaa                           >  1:128988/1‑140 (MQ=255)                                                                                                                 tCAAACGCGTTGAAAAAAAAAACAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTCAAg                          <  1:66536/140‑1 (MQ=255)                                                                                                                  cAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGa                         >  1:1028591/1‑140 (MQ=255)                                                                                                                  cAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGa                         >  1:632932/1‑140 (MQ=255)                                                                                                                     aCGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAg                      <  1:483940/140‑1 (MQ=255)                                                                                                                      cgctTTAAAAAAAAAAAAAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGc                     <  2:301618/140‑1 (MQ=255)                                                                                                                      cgcgTTAAAAAAAAAAAAAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGc                     <  2:1072503/140‑1 (MQ=255)                                                                                                                         gTTGAAAATAAAAACAAAAC‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGAc                  <  1:1230040/140‑1 (MQ=255)                                                                                                                          ttGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGAcc                 >  1:653984/1‑140 (MQ=255)                                                                                                                                    aaaaaaaac‑cCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGc       <  2:653984/140‑1 (MQ=255)                                                                                                                                         aaac‑cCCGCCGAAGCGGGTTAAGTGGGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGtt  <  2:240348/140‑1 (MQ=255)                                                                                                                                         aaac‑cCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGtt  <  2:1028591/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                          TTCATCATCAGAATCCTTCCGGATAATTAGCTCTCCCCTTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAA‑CCCGCCGAAGCGGGTTAAGTGCGGGTGCGTTGAGGATGCCTGCCACATCAGAGGTGGCGAGGGATTTCTCCCCCGCCGGGTCTCTTACTCCTCAGGTTCGTAAGCTGTGAAGACAGCGACCTCCGTCTGGCCGGTT  >  NC_000913/1644895‑1645170

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑