Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	226,530	0	C	A	67.9%	54.6 / 65.1	56	noncoding (772/2904 nt)	rrlH	23S ribosomal RNA of rrnH operon
Reads supporting (aligned to +/- strand):  ref base C (7/11);  new base A (23/15);  total (30/26)
Fisher's exact test for biased strand distribution p-value = 1.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.02e-02

GGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATAC  >  NC_000913/226454‑226679                                                                             |                                                                                                                                                       ggCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAAc                                                                              <  1:603770/151‑1 (MQ=11)         gAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTc‑c                                                                     >  1:366758/1‑151 (MQ=31)               taggTAACACTGACTGGAGGACCGAACCCACTCCCGTTGAAAAGGTAGGGGATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATgtatcactctggg                                                                     >  1:209556/3‑134 (MQ=0)               taggTAACACTGACTGGAGGACCGAACCCACTCCCGTTGAAAAGGTAGGGGATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATgtatcactctggg                                                                     <  2:209539/144‑13 (MQ=0)                gggTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGt                                                               <  2:274170/150‑1 (MQ=31)                 ggTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTag                                                             <  1:442925/151‑1 (MQ=31)                    aaCACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGc                                                          >  1:687420/1‑151 (MQ=31)                      cacTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCAc                                                        <  2:176382/151‑1 (MQ=31)                           aCTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGttt                                                   >  2:300773/1‑151 (MQ=31)                            cTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTc                                                  >  2:37725/1‑151 (MQ=31)                              ggaggaCCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTc                                                  <  2:729531/149‑1 (MQ=31)                              ggaggaCCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCgg                                                <  1:70505/151‑1 (MQ=31)                              ggaggaCCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCgg                                                >  1:702472/1‑151 (MQ=31)                                   accgaaccgaCTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAgg                                           <  2:699605/151‑1 (MQ=31)                                   accgaacccaCTCCCTTTGAAAAGGTAGGGGATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATgtatcactctg                                                                       >  1:66878/1‑114 (MQ=0)                                   accgaacccaCTCCCTTTGAAAAGGTAGGGGATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATgtatcactctg                                                                       <  2:66871/124‑11 (MQ=0)                                    ccgaacccaCTCCCGTTGAAAAGGTAGGGGATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATgtatcactctggg                                                                     >  1:361379/1‑113 (MQ=0)                                    ccgaacccaCTCCCGTTGAAAAGGTAGGGGATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATgtatcactctggg                                                                     <  2:361341/125‑13 (MQ=0)                                              tAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCg                                >  1:685312/1‑151 (MQ=31)                                                        aaaTTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAAc                      <  2:720420/151‑1 (MQ=31)                                                             aGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGAt                 >  2:44732/1‑151 (MQ=31)                                                             aGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGAt                 <  2:783043/151‑1 (MQ=31)                                                               gggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGc                                               <  1:60973/117‑1 (MQ=0)                                                               gggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGc                                               >  2:60966/2‑118 (MQ=0)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGt                                                     >  2:312736/1‑111 (MQ=0)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGt                                                     <  1:312767/111‑1 (MQ=0)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCgg                                                <  1:383960/116‑1 (MQ=0)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCgg                                                >  2:383920/1‑116 (MQ=0)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGc                                               >  2:242605/1‑117 (MQ=0)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGc                                               <  1:242630/117‑1 (MQ=0)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCa              >  1:110064/1‑150 (MQ=1)                                                                ggATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCa              >  2:230610/1‑150 (MQ=1)                                                                ggATAACTTGTGGAACGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCa              >  1:282477/1‑150 (MQ=0)                                                                 gATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGct                                              <  1:144954/117‑2 (MQ=0)                                                                 gATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCaa             >  1:724366/1‑150 (MQ=1)                                                                 gATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCaa             >  2:173217/1‑150 (MQ=1)                                                                 gATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTAGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAggg                                          >  1:334698/1‑121 (MQ=0)                                                                 gATGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTAGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAggg                                          <  2:334662/121‑1 (MQ=0)                                                                  aTGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAgggggcc                                      <  1:398972/124‑3 (MQ=0)                                                                  aTGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAgggggcc                                      >  2:398932/1‑122 (MQ=0)                                                                  aTGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCAAAc           <  1:173230/151‑1 (MQ=1)                                                                  aTGACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTACTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCAAAc           >  2:275068/1‑151 (MQ=1)                                                                    gACTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCAAACtc         >  1:391795/1‑150 (MQ=1)                                                                      cTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGcta                                             <  2:352854/113‑3 (MQ=0)                                                                      cTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGcta                                             >  1:352892/1‑111 (MQ=0)                                                                      cTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGc                                               >  2:123981/1‑111 (MQ=0)                                                                      cTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGc                                               <  1:123993/111‑1 (MQ=0)                                                                      cTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAgg                                           <  2:32326/115‑1 (MQ=0)                                                                      cTTGTGGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAgg                                           >  1:32331/1‑115 (MQ=0)                                                                        tgtgGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCgg                                                <  2:354666/108‑1 (MQ=0)                                                                        tgtgGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCgg                                                >  1:354704/1‑108 (MQ=0)                                                                        tgtgGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCAAACTCCGa      >  2:137510/1‑150 (MQ=1)                                                                         gtgGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGa      <  1:526095/150‑1 (MQ=31)                                                                         gtgGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCAAACTCCGaa     >  1:255553/1‑150 (MQ=1)                                                                         gtgGATCGGAGTGAAAGGCTAATCAAGCTCGGAGATAGCTGGTTCTCCTCGAAAGCTATTTAGGTAGCGCCTCATGTA‑TCA‑CTCTGGGGGGTAGAGCACTGTTTCGGCTAGGGGGTCATCCCGACTTACCAAACCGATGCAAACTCCGAAt    >  2:343317/1‑151 (MQ=1)                                                                            gCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATAc  <  2:189193/151‑1 (MQ=31)                                                                             |                                                                                                                                                       GGCAGGTTGAAGGTTGGGTAACACTAACTGGAGGACCGAACCGACTAATGTTGAAAAATTAGCGGATGACTTGTGGCTGGGGGTGAAAGGCCAATCAAACCGGGAGATAGCTGGTTCTCCCCGAAAGCTATTTAGGTAGCGCCTCGTGAACTCATCTC‑CGGGGGTAGAGCACTGTTTCGGCAAGGGGGTCATCCCGACTTACCAACCCGATGCAAACTGCGAATAC  >  NC_000913/226454‑226679

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑