Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,200	0	G	A	46.2%	51.2 / 27.3	52	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base G (24/4);  new base A (0/24);  total (24/28)
Fisher's exact test for biased strand distribution p-value = 4.96e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTG  >  NC_000913/3556051‑3556347                                                                                                                                                       |                                                                                                                                                    ccAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGa                                                                                                                                                    <  1:110958/151‑1 (MQ=255)           cGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTcc                                                                                                                                            >  2:665568/1‑149 (MQ=255)             cAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGc                                                                                                                                        >  1:244617/1‑151 (MQ=255)              aaCCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGcc                                                                                                                                       >  2:908709/1‑151 (MQ=255)                  accTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAgtg                                                                                                                                   >  2:551117/1‑151 (MQ=255)                       ggcccggccgcgTTTTCCACGGACAACAAAAAGGTGTTCGGTGATTTTTTCTTTTCCGACTTCAGGCAAGACGTTTTACCCCGCCCCCTGGTCGCGCGGCAGGTTAGGAATTTTCTTTC‑CTGGCAGGAAAAACCCCCCCGCCAGTGTAGc                                                                                                                               <  2:677800/142‑1 (MQ=255)                          aCTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGAtt                                                                                                                           >  2:599888/1‑151 (MQ=255)                          aCTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGAtt                                                                                                                           >  1:255943/1‑151 (MQ=255)                            tGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTc                                                                                                                         >  2:330592/1‑151 (MQ=255)                            ggccgcgTTTTTCACCAACAAAAAAAAAGCGTTCGGTGATTTTTCCACTTTCGACTTAAAGCGAGACGTTATTCCCCGGCCCCTGGCCGCGCGGCAGTTTATAAATATTCTTTT‑AATGCAGGAAAAAACTCCCCGCCAGTGTAGCGATTTc                                                                                                                         <  2:688665/148‑1 (MQ=255)                              aCGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCAc                                                                                                                       >  1:716464/1‑151 (MQ=255)                              aCGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCAc                                                                                                                       >  1:552658/1‑151 (MQ=255)                               cgcgCTTTCCCCCGACAAAAAAAAAGCTTTGGTTGATTTTTTCCCTTCCGACTTAAAGCGGGAGGTTATTCCCGGTCCCCTGGTCGCGCGGCAGGTTATAAATTTTCTTTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCAc                                                                                                                       <  1:597276/150‑1 (MQ=255)                                gcgcTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGGGAGACGGTATCCCCCGGCCCCTGGCCGCGCGGCAGGTTATGAATTTTCTGTT‑CAGGCAGGGAAAACCCCCCCGCCAGTGTAGCGATTTCACg                                                                                                                      <  2:79054/150‑1 (MQ=255)                                   cTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTc                                                                                                                   >  1:685816/1‑150 (MQ=255)                                    ttttCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTc                                                                                                                   >  1:204865/1‑149 (MQ=255)                                    tttcCACCGACAAAAAAAAAGCGTTGGGTAATATTTTCCCTTCCGACTCCAAGCGAGACGTTTTTCCCCGGCCCCGGGTCGCGCGGCAGTTTAAAAATTTTCTGTT‑CATGCAGGAAAAAACCCCCCGCCAGTGTAGCGATTTCa                                                                                                                        <  2:752252/144‑1 (MQ=255)                                            gacgacAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATgg                                                                                                         >  2:85532/1‑151 (MQ=255)                                                aaaaaaagGCGTGCGGTGATATTTTCCTTTCCGACTCCAAGCGGGGCGTTATTCCCCGCCCCCTGGCCGCGCGGCGGTTTATAAATTTTTGTTT‑CAGGCGGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc                                                                                                        <  2:385817/146‑1 (MQ=255)                                                     aaggCGTTGGTTAATATTTTCCCTTCCGATTTAAAGCGAGCCGTTATTCCCCGGCCCGTGGCCGCGGGGCAGTTTATGATTATTCTGTT‑CAGGCAGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGcaca                                                                                                <  2:204222/148‑1 (MQ=255)                                                       aGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACAcc                                                                                              >  1:158860/1‑151 (MQ=255)                                                        gCGTTGGGTGATTTTTTCCTTTTCGCCTTCAGGGGAGACGTTATTCCCCGGCCCCTGGTCGCGCGGCAGGTTATGAATTTTCTTTT‑CATGCGGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACAcc                                                                                              <  1:356014/150‑1 (MQ=255)                                                           ttggttGATTTTTTCTCTTGCGACTCAAAGGGAGCGGTTTTTCCCCGCCCCCTGGCCGCGCGGCGGTTTATAAATTTTTTTTT‑CATGGAGGAAAACCCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCacac                                                                                               <  2:977669/141‑1 (MQ=255)                                                           ttCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCt                                                                                          >  1:749167/1‑151 (MQ=255)                                                                   ttttttCTCTTTCGACTTAAAGCAGGCGGGTATTCCCCGGCCCCGGGTCGCGCGGCGGGTTATAAATATTCTGTT‑CAGGCAGGGAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGa                                                                                    <  2:137028/147‑1 (MQ=255)                                                                   tatTTTCCTTTTCGACTTCAAGCGAGAGGTTATTCCCCGCCCCCTGGCCGCGCGGCAGTTTATAAATATTCTGTT‑CAGGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCt                                                                                          <  1:728190/143‑1 (MQ=255)                                                                      tttCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTtc                                                                               >  2:715203/1‑151 (MQ=255)                                                                      tttCACTTTCGACTAAAAGGGAGACGGTATTCCCCGGCCCCGGGTCGCGGGGCGGTTTATGAATTTTCTGTT‑AATGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACtt                                                                                <  1:410456/150‑1 (MQ=255)                                                                       ttccttttCGCCTTCAAGCGAGACGGTATTCCCCGCCCCCTGGTCGCGCGGCGGGTTATGAATATTCTGTT‑CATGCAGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTtc                                                                               <  1:789350/145‑1 (MQ=255)                                                                            tttCGTCTCAAAGCGAGACGGTATTCCCCGGCCCCTGGTCGCGCGGCAGTTTATGAATTTTCTGTT‑CATGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTcc                                                                            <  2:183807/148‑1 (MQ=255)                                                                              tCGTCTACAAGCGAGACGGTATTCCCCGGCCCCTGGTCGCGCGGCGGTTTATGAATTTTCTGTT‑CATGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCAc                                                                          <  2:774958/148‑1 (MQ=255)                                                                                 aCTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCt                                                                    >  2:501760/1‑151 (MQ=255)                                                                                      aaGCGAGCCGGTATTCCCCGCCCCCTGGTCGCGCGGCGGTTTAGAAATTTTCTGTT‑CAGGAAGGAAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCt                                                                    <  1:577992/146‑1 (MQ=255)                                                                                        gCGAGACGGAATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAAt                                                             >  2:579840/1‑151 (MQ=255)                                                                                             aCGTTATTCCCCGGCCCGGGGTCGCGCGCCAGTTTATAAATATTCTGTT‑CATGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGt                                                           <  1:855705/148‑1 (MQ=255)                                                                                               gttATTCCCCGGCCCCTGGTCGCGCGGCAGTTTATGAATATTCTGTT‑CATGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTccc                                                       <  1:134508/148‑1 (MQ=255)                                                                                               gttATTCCCCGCCCCCTGGTCGCGCGGCAGTTTATAAATATTCTGTT‑CATGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTccc                                                       <  1:596890/148‑1 (MQ=255)                                                                                               ggTATCCCCCGGCCCTTGGCCGCGCGGCAGTTTATAAATATTTTTTT‑CAGGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcg                                                      <  1:962194/151‑1 (MQ=255)                                                                                                   tcccccGGCCCCTGGTCGCGCGGCAGGTTATAAATATTCTTTT‑CATGAAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTcc                                                        <  1:721500/142‑1 (MQ=255)                                                                                                    tACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTc                                                 >  1:286100/1‑151 (MQ=255)                                                                                                      cccGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGc                                               >  1:226342/1‑151 (MQ=255)                                                                                                      cccGCCCCTGGGTCGCGCGGCAGTTTTTAAATCTTCTTTC‑CAGGTAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTAAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCt                                                  <  1:29788/148‑1 (MQ=255)                                                                                                           ccccGGGCCGCGCGGCAGTTTAGGAATATTCTGTT‑CAGGCAGAAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCaa                                            <  2:244613/149‑1 (MQ=255)                                                                                                               tGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGc                                       >  2:802322/1‑150 (MQ=255)                                                                                                                ggTCGCGCGGCAGGTTAAAAATA‑TCTGTTCCAGGGGGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCaa                                     <  1:294965/151‑1 (MQ=255)                                                                                                                           aGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACg                          >  1:839053/1‑151 (MQ=255)                                                                                                                            gttaaTGAATTTTTTTTT‑CATGAAGGAAAAAACCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTaaa                            <  1:251238/144‑1 (MQ=255)                                                                                                                              ttATAAATTTTCTTTT‑CAGGCGGGAAAACCCCCCCCGCCAGTGTAGCGATTTCGCGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGAt                        <  2:743460/150‑1 (MQ=255)                                                                                                                                   aaTATTCTGTT‑CAGGCAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCa                    <  1:518231/149‑1 (MQ=255)                                                                                                                                           gTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCGCACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGAc          >  2:278085/1‑151 (MQ=255)                                                                                                                                               cATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTc       >  1:532279/1‑151 (MQ=255)                                                                                                                                                    aGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCGTCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTg  >  2:874274/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                    CCAACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTG  >  NC_000913/3556051‑3556347

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: ‑