Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,207	0	T	C	46.3%	69.2 / 17.0	54	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base T (26/3);  new base C (0/25);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.96e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCACACC  >  NC_000913/3556061‑3556357                                                                                                                                                    |                                                                                                                                                       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                                                                                                                                     >  1:255943/1‑151 (MQ=255)                aCTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGAtt                                                                                                                                     >  2:599888/1‑151 (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)                                                                                                                                           ggaaaaacCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGtt             <  1:85536/146‑1 (MQ=255)                                                                                                                                                aaaCTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGccacc       >  1:395644/1‑150 (MQ=255)                                                                                                                                                   cTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCacac   >  2:633007/1‑151 (MQ=255)                                                                                                                                                    tCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCACAcc  >  2:556091/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                       CGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTT‑CATGCAGGGAAAAACTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCACACC  >  NC_000913/3556061‑3556357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑