Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,200	0	G	A	43.8%	49.8 / 20.2	48	S217F (TCC→TTC)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base G (20/7);  new base A (0/21);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 8.13e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCC  >  NC_000913/3556054‑3556349                                                                                                                                                   |                                                                                                                                                       aCTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGaaaa                                                                                                                                                    <  1:576485/151‑1 (MQ=255)  cTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGaaaa                                                                                                                                                    >  2:225798/1‑150 (MQ=255)    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)                                                                                                                                                  ggAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGcc  >  2:589755/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                       ACTGTGCCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCC  >  NC_000913/3556054‑3556349

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: ‑