Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,684,749	0	A	C	42.3%	76.8 / 11.8	53	D164A (GAC→GCC)	tus	inhibitor of replication at Ter, DNA‑binding protein
Reads supporting (aligned to +/- strand):  ref base A (25/5);  new base C (0/22);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 3.07e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGAGCG  >  NC_000913/1684606‑1684899                                                                                                                                                  |                                                                                                                                                       caTCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGcc                                                                                                                                                 <  2:847495/151‑1 (MQ=255)         aaCTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACg                                                                                                                                         >  2:331966/1‑151 (MQ=255)              aaGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCAGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTttg                                                                                                                                    >  1:769862/1‑151 (MQ=255)                gACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTttggt                                                                                                                                  >  1:1089840/1‑151 (MQ=255)                   cACGTTCGCGCTTTCCGTCACGGTTAAATCAAACCCCCCCCCCGCGGCCGGTTTTGAGTGGGTCCCCGGTC‑TTTTCCGGGGCTTAATCCCCTTTATTCCTTCCCCA‑ACGCACACCGTCCTCCACCCCCCCGCCACTTTACGCTttg                                                                                                                                    <  1:883132/146‑1 (MQ=255)                      gTTCGAGCATATCGTCACGGTTGAATCAGACCCCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCTTTTGCCGGGGC‑TGATCCCCCTTAATGCTTACCGC‑CCGCTCCCCGTTCTGCACTCCCCCGCCACTTTACGCTTTGGTTGGGCt                                                                                                                            <  1:795558/151‑1 (MQ=255)                            gCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCtaataa                                                                                                                       >  1:811248/1‑150 (MQ=255)                               taccGTCAGGTTTGAATCAGACCCCCCCCCCGCGGCACGTTTTGAATGGTTGCTTCGTCTTTTGCCGGGGT‑TGACCCCCTTTAATGCTTCCCGC‑ACGCTCACCTTTCTCCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATaaa                                                                                                                      <  2:1209603/145‑1 (MQ=255)                                   gTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATc                                                                                                                >  2:1168687/1‑150 (MQ=255)                                     cgcGGTTGAATCAGACCCCCCCCCCGCGGCACTTTTTGAATGGGTGCATCTTCTTTTGCGGGGGC‑TGATCCCCCTTAATGTTTCCCGC‑CCGCTCCCCTTTCGGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCAtt                                                                                                             <  2:279101/149‑1 (MQ=255)                                     ccgggTTGAATCAAACCTCCCCCCCGCGGCACGTTTGGAAGGGGGGCCTCTTTTTTTCCCGGGGC‑TGATCCCCCTTAATGTTTCCCGC‑CCGCTCACCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCAtt                                                                                                             <  2:802450/148‑1 (MQ=255)                                      aCGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCAtt                                                                                                             >  2:128537/1‑150 (MQ=255)                                        ggTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTa                                                                                                            >  2:1244956/1‑149 (MQ=255)                                        ggTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTa                                                                                                            >  2:458104/1‑149 (MQ=255)                                        ggTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTa                                                                                                            >  1:1063387/1‑149 (MQ=255)                                        ggTTAAATCAGACCCCCCCCCCGCGGCATGTTTTAAATGGTGGCATCTTCTTTGGCCGGGGC‑AGACCACCTTTAATGTTTCCCGC‑CCGCTCACCGATCTACCCACCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTaa                                                                                                           <  1:1054194/150‑1 (MQ=255)                                         gTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTa                                                                                                            >  1:1050103/1‑148 (MQ=255)                                                   acccccccACCGCGGCCTGTTTTGAATGGTGGCATCGTTTTTTGCCGGGTC‑TGATCCCCCTAATTGCTTCCCCC‑ACCTCCCCCGTTCGGCGCGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATc                                                                                                <  2:1107459/146‑1 (MQ=255)                                                    accccccccCGCGGCACTTTTTAATTGGGTGCATCGTCTTTTGCCGGGGC‑TGATCCCCCTTATTGCTTCCCGC‑ACGCCCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCg                                                                                               <  2:990566/147‑1 (MQ=255)                                                         cccccGCGGCCCGTTTTGAAGGGGTGTATCTTTTTTTGCCGGGGC‑TGTTCCCCTTAAATGCTTCCCGC‑CCCCTCCCCTTTCTGCACCCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGtgatga                                                                                         <  2:1248837/148‑1 (MQ=255)                                                          ccccGCGGCACTTTTTGAATGGGTGCATCGTCTTTTGCGGGGGC‑TGACCCCCCTTATTGCTTCCCGC‑ACGCTCACCGTTCTGCACCCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGaa                                                                                        <  1:1206213/149‑1 (MQ=255)                                                              gcgGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGCTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTcc                                                                                    >  2:913844/1‑151 (MQ=255)                                                                     tttttAAAGGGGTGAATTGTCTTTTCCGGGGTC‑GGACCCCCTTTATTGGTTCCCGC‑ACTCTAACCGTCATCCAAGCCACCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGcac                                                                              <  1:458411/149‑1 (MQ=255)                                                                        ttGAGTGGGTCCATCGTCATTTGCCGGGCC‑TGACCCCCTTTAATGCTTCCCGC‑ACCCTCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAg                                                                            <  1:749897/149‑1 (MQ=255)                                                                           ctctccccctctttCATTTGCGGGGGC‑TGACCACCCTTATTTCTTCCCGC‑CCGCCCCCTTTCCTGCCCACCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGc                                                                           <  1:451943/134‑1 (MQ=255)                                                                           aaggggTGCATCGTCTTTTGCCGGGGC‑TGACCCCCCTTAATGCTTCCCGC‑CCCCTCCCCGTTCGGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTgg                                                                        <  2:363016/147‑1 (MQ=255)                                                                           aaTGGGTGCATCTTCATTTCCCGGGGC‑TGATCCCCCTTAATGTTTCCCGC‑CCGCCCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTg                                                                         <  2:437289/149‑1 (MQ=255)                                                                              ggggGCATCGTCTTTGGCGGGGGC‑TGATCCCCTTTAATGCTTCCCGC‑ACGCCCCCCTTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGaa                                                                      <  2:344508/149‑1 (MQ=255)                                                                                       gTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGc                                                                           >  2:451954/1‑135 (MQ=255)                                                                                       gTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGa                                                            >  1:1220579/1‑150 (MQ=255)                                                                                       gTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGa                                                            >  2:677585/1‑150 (MQ=255)                                                                                       gTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGa                                                            >  1:280555/1‑150 (MQ=255)                                                                                          aTTTGCCGGGGC‑TGATCAGCGTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACACCGCCACTTTACGCTTTGGCTGGGCTAATAAACATATCATGAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATc                                                        >  1:902803/1‑151 (MQ=255)                                                                                           tttGCCGGGGC‑TGACCCCCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGaa                                                           <  1:925381/147‑1 (MQ=255)                                                                                           tttGCCGGGGC‑TAACCCCCCTTAATGCTTCCCCC‑GCGCTCACCTTTCTCCACACCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGaa                                                           <  2:838365/147‑1 (MQ=255)                                                                                               ccGGGGC‑TGATCCCCCTTAATTCTTCCCGC‑ACGCTCCCCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATcaccac                                                   <  2:1173880/151‑1 (MQ=255)                                                                                               ccGGGCC‑TGCTCCCCTTTAATGCTT‑CCGCAACGCACACCTTTCGCCACAGCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATcacca                                                    <  1:474071/150‑1 (MQ=255)                                                                                                cGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACg                                                  >  2:1133708/1‑151 (MQ=255)                                                                                                 ggggC‑TGATCCCCCTTAATGCTTCCCGC‑CCGCCCCCCTTTCTGCCCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACg                                                  <  2:183140/150‑1 (MQ=255)                                                                                                    gC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAgt                                              >  2:413297/1‑151 (MQ=255)                                                                                                         aTCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCg                                          >  1:449444/1‑151 (MQ=255)                                                                                                           cACCCTTAATGCTTCCCGC‑ACGCTACCCGTTCTCCCCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTc                                           <  1:979321/148‑1 (MQ=255)                                                                                                             cccTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCAcc                                      >  2:949564/1‑151 (MQ=255)                                                                                                                 tAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTgg                                  >  2:1025017/1‑151 (MQ=255)                                                                                                                    tgtttcccGC‑TCGCTCGCCGTTCGCCGCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGAc                                <  1:290485/144‑1 (MQ=255)                                                                                                                      cTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGAcgcg                             >  2:178802/1‑151 (MQ=255)                                                                                                                          ccGC‑ACCCTCCCCTTTCTGCACTCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCgag                         <  2:811283/151‑1 (MQ=255)                                                                                                                           ccccccGCTCTCCGTTCTGCCCGACTCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGAcgcgc                            <  2:491191/143‑1 (MQ=255)                                                                                                                                 gCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTgg                   >  2:1106260/1‑151 (MQ=255)                                                                                                                                 gCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGCGTCGCACCGTGGACGCGAGAGGAGTgg                   >  2:173229/1‑151 (MQ=255)                                                                                                                                  cTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGc                  >  2:522538/1‑151 (MQ=255)                                                                                                                                         ttCTGCCCGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGaa            <  2:571733/150‑1 (MQ=255)                                                                                                                                         tccagcatcaCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAATaa            <  1:566882/141‑1 (MQ=255)                                                                                                                                           ctccaccacCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGaa            <  1:975339/145‑1 (MQ=255)                                                                                                                                              cACGCCCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACt        <  2:316529/149‑1 (MQ=255)                                                                                                                                                  aCCCCGCAACTTTAAGCTTTAGTTGGGCTAATAAACATATCATGAAGAATTTACATCGCGATGACGTCCTGGAACAGCTGGAAAAAAGCCTGAAATAACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGAGCg  >  1:1062916/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                       CATCAATAAACTCAAGACCACGTTCGAGCATATCGTCACGGTTGAATCAGAACTCCCCACCGCGGCACGTTTTGAATGGGTGCATCGTCATTTGCCGGGGC‑TGATCACCCTTAATGCTTACCGC‑ACGCTCACCGTTCTGCACGACCCCGCCACTTTACGCTTTGGTTGGGCTAATAAACATATCATTAAGAATTTACATCGTGATGAAGTCCTGGCACAGCTGGAAAAAAGCCTGAAATCACCACGCAGTGTCGCACCGTGGACGCGCGAGGAGTGGCAAAGAAAACTGGAGCG  >  NC_000913/1684606‑1684899

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: ‑