Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,207	0	T	C	42.3%	63.2 / 17.2	52	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base T (23/7);  new base C (0/22);  total (23/29)
Fisher's exact test for biased strand distribution p-value = 8.45e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCACAC  >  NC_000913/3556057‑3556356                                                                                                                                                        |                                                                                                                                                      gtgCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑Ct                                                                                                                                                       <  1:636975/151‑1 (MQ=255)  tgCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTc                                                                                                                                                      >  2:106593/1‑151 (MQ=255)        aaCCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGcc                                                                                                                                                >  1:261657/1‑151 (MQ=255)          cccccTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCa                                                                                                                                               <  2:22454/147‑1 (MQ=255)            accTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAgtg                                                                                                                                            >  1:150633/1‑151 (MQ=255)                 ggCATTGACGCGTTTTCCACCGACAAAAAAAAAGCGTGCGGTGATATTTTCACTTTCGCCTTAAAGGGAGACGGTATTCCCCGGCCCCGGGTCGCGCGGCAGGTTATAAATATTCTGTTCATGAAGGGAAAAA‑CTCCCCGCCAGTGTAGc                                                                                                                                        <  2:60703/150‑1 (MQ=255)                           cgttttcccccGACGAAAAAAAAGCTTTCGGTGATTTTTCCACTTTCGACTTCACGCGAGCCTTTTTTCCCCGCCCCCTGGTCGCGCGGCAGTTTATAAATATT‑TTTTCCTTGAGGGAAAAATCTCCCCGCCAGTGTAGCGATTTCACGc                                                                                                                              <  1:639514/141‑1 (MQ=255)                               tttCCCCGACGAAAAAAAAGCTTTGTGGAATTTTTTCACTTTCGACTAAAAGCGAGCCGGTTTTCCCCGCCCCCTGGCCGCGCGGCAGTTTATGAATATTCTGTTCATGGAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCa                                                                                                                           <  1:100482/149‑1 (MQ=255)                                ttCACCGACGAAAAAAAAGCGTTGGGTGATTTTTTCACTTCCGCCTCAAAGCGAGACGTTATTCCCCGGCCCCGGGTCGCGCGGCAGTTTATAAATATTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGc                                                                                                                         <  1:672844/150‑1 (MQ=255)                                    cccacaaaaaaaaaGCTTTCGGTGATTTTTCCCCTTTCGCCTCAAAGCGAGACGGTTTTCCCCGCCCCCTGCCCGGGCGGCAGTTTATGAATATTCTTTTCATGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAt                                                                                                                    <  2:300337/143‑1 (MQ=255)                                      gacgacAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATgg                                                                                                                  >  1:308825/1‑151 (MQ=255)                                       acgacAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc                                                                                                                 >  1:379876/1‑151 (MQ=255)                                       acaaaaaaaagGCGTTCGGTTATTTTTTCACTTCCGACTTCAGGCGAGAGGGTATTCCCCGCCCCCTGGCCGCGCGGCGGTTTATAAATATTTTTTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATg                                                                                                                   <  2:300476/144‑1 (MQ=255)                                        caaaaaaaaaGCGTCCGGTAATATTTTCCCTTTCAACTGAAGGCGAGACGGTATTCCCCGCCCCCTGGCCGCGCGGCAGGTTATAAATTTTCTTTTCATGCAGGAAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATgg                                                                                                                  <  2:121036/145‑1 (MQ=255)                                           cAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCgg                                                                                                             >  1:580585/1‑151 (MQ=255)                                              aaaaGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGcac                                                                                                          >  1:671736/1‑151 (MQ=255)                                                  gctttCGGTGATATTTTCCTTTGCGACTACAAGCGAGACGTTTTTCCCCGGCCCCTGGTCGCGCGGCAGGTTATAAATATTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCa                                                                                                      <  2:664165/148‑1 (MQ=255)                                                     ttggttgtttttttCCCTTTCGCCTCCAGGGGATCCGGTTTTCCCCGGCCCCTGGCCGCGCGGCAGTTTATAAATATTCTTTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCa                                                                                                      <  1:6396/138‑1 (MQ=255)                                                     ttgggTGATTTTTTCCTTTTCGATTCCAGGGGAGACGTTTTTCCCCGGCCCCGGGTCGCGCGGCGGGTTATAAATATTTTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAg                                                                                                     <  1:194906/146‑1 (MQ=255)                                                             ttttttCCCTTCCGACTTAAAGCGAGACGGTTTTCCCCGGCCCCTGGCCGCGCGGCAGTTTATGAATATTCTTTTCATGCGGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATa                                                                                               <  1:656921/145‑1 (MQ=255)                                                             tatTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAAc                                                                                           >  1:280925/1‑151 (MQ=255)                                                              atTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACt                                                                                          >  1:499460/1‑151 (MQ=255)                                                                 ttCACTTTCGACTTCAAGCGAGACGGTATTCCCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTtc                                                                                        <  1:531306/150‑1 (MQ=255)                                                                 ttCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTtct                                                                                       >  1:324006/1‑151 (MQ=255)                                                                      tttCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACg                                                                                  >  1:286809/1‑151 (MQ=255)                                                                      tttCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACg                                                                                  >  1:523484/1‑151 (MQ=255)                                                                       ttCGACTTCAGGCGAGACGGTTTTCCCCGGCCCCGGGTCGGGCGGCAGTTTATGAATATTCTGTTCAGGGAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACg                                                                                  <  1:33453/150‑1 (MQ=255)                                                                       tgcgcctccAAGGGGGAGGGTATTCCCCGGCCCCGGGCCGGGCGGCAGGTTATGAATATTCTTTTCAGGAGGGGAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACg                                                                                  <  1:67210/142‑1 (MQ=255)                                                                          gACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATc                                                                              >  1:400802/1‑151 (MQ=255)                                                                                aaccGAGACGGTATTACCCGGCCCCTGGGCGCGCGGCAGGTTATGAATATTCTGTTCACGCAGGGCAATA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGc                                                                           >  2:24768/4‑148 (MQ=255)                                                                                  gCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAAt                                                                      >  2:509345/1‑151 (MQ=255)                                                                                    gagaCGGTATTCCCCGGCCCCTGGTCGCGCGGCAGTTTATGAATATTCTTTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACaa                                                                       <  1:480797/148‑1 (MQ=255)                                                                                            aTTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCgcgc                                                            >  2:666308/1‑151 (MQ=255)                                                                                               ccccGGCCCCGGGTCGCGCGGCAGGTTATGAATATTCTTTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTc                                                          <  2:486231/149‑1 (MQ=255)                                                                                                cccGGCCCCTGGTCGCGCGGCGGGTTATAAATTTTCTGTCCAGGCGGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGc                                                        <  2:230685/151‑1 (MQ=255)                                                                                                cccGCCCCCGGGCCGCGCGGCAGTTTATAAATTTTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTc                                                          <  1:395974/149‑1 (MQ=255)                                                                                                     ccccTGGGCGCGGGGCAGGTTATAAATTTTCTGTCCAGGCGGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCa                                                      <  2:273168/148‑1 (MQ=255)                                                                                                       ccTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTg                                                 >  2:597018/1‑151 (MQ=255)                                                                                                                gcgGCAGGTTATAAATTTTTTGTTCATGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAgg                                            <  1:569882/147‑1 (MQ=255)                                                                                                                     aGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACg                                   >  2:488131/1‑151 (MQ=255)                                                                                                                        ttATGAATATTCTTTTCATGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGAt                                 <  1:184624/150‑1 (MQ=255)                                                                                                                             aaTATTCTGTTCATGGAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGcc                              <  1:262657/148‑1 (MQ=255)                                                                                                                                 ttttGTCCATGCAGAAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACggg                         <  2:91430/146‑1 (MQ=255)                                                                                                                                   cTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCg                       >  1:701418/1‑149 (MQ=255)                                                                                                                                    tGTTCAGGCAGGAAAAAC‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCgag                     <  1:391601/150‑1 (MQ=255)                                                                                                                                      ttCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCga                      <  1:266620/147‑1 (MQ=255)                                                                                                                                              ggaaaaac‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCg              <  1:84413/144‑1 (MQ=255)                                                                                                                                               ggAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGcc         >  2:589755/1‑151 (MQ=255)                                                                                                                                                 aaaac‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTcc               <  2:11716/143‑1 (MQ=255)                                                                                                                                                     a‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCcaccac    >  1:285465/1‑150 (MQ=255)                                                                                                                                                     a‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCcaccac    >  1:155484/1‑150 (MQ=255)                                                                                                                                                       cTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACcaca   <  2:421711/150‑1 (MQ=255)                                                                                                                                                       cTCCCCGCCAGTGTAGCGAATTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCacac  >  2:105299/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                      GTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACCACAC  >  NC_000913/3556057‑3556356

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: ‑