Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,556,207	0	T	C	42.9%	54.6 / 15.5	42	S215G (AGT→GGT)	rtcA	RNA 3'‑terminal phosphate cyclase
Reads supporting (aligned to +/- strand):  ref base T (23/1);  new base C (0/18);  total (23/19)
Fisher's exact test for biased strand distribution p-value = 5.37e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACC  >  NC_000913/3556060‑3556352                                                                                                                                                     |                                                                                                                                                  ccGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTccc                                                                                                                                                >  2:353271/1‑151 (MQ=255)    cAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGc                                                                                                                                             >  1:634386/1‑151 (MQ=255)                  cTGACGCGCTTTTCACCGACGCCAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGAttt                                                                                                                               >  1:377002/1‑151 (MQ=255)                      cgcgCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACg                                                                                                                           >  1:360489/1‑151 (MQ=255)                           tttcccccGACAAAAAAAAAGCTTGCGGTAATTTTTTCCCTTTCGACTTAAAGCGAGAGGGTTTTCCCCGCCCCCGGGCCGCGCGGCGGTTTATAAATATTCTGTTCATGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGc                                                                                                                          <  2:571276/141‑1 (MQ=255)                              tCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCa                                                                                                                    >  2:574666/1‑150 (MQ=255)                              tCACCGACGACAAAAAAGCGTTCGGTGATATGTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCa                                                                                                                    >  1:646001/1‑150 (MQ=255)                               ccccGACAAAAAAAAAGCGTTCGGTGATTTTTCCACTTTCGACTCCAAGCGAGCCGTTTTCCCCGGGCCCCGGGCCGCGCGGCAGGTTATGAATATTCTTTTCGTGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCaa                                                                                                                   <  1:48241/148‑1 (MQ=255)                                  cgacaaAAAAAAAGCTTTCGGTATTTTTTTCCTTTCCGACTTAAAGCGAGAGGTTTTTCCCCGCCCCTTGGTCGCGCGGCAGTTTATAAATTTTTTTTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACAt                                                                                                                <  2:467155/150‑1 (MQ=255)                                    acgacAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGgc                                                                                                             >  1:642611/1‑151 (MQ=255)                                          aaaaaGCTTTGGGTGATTTTTTCCCTTTCGACCCAAAGCAAGACGTTATTCCCCGCCCCCTGGCCGCGCGGCAGGTTATAAATATTCTGTTCAGGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGca                                                                                                       <  1:253631/151‑1 (MQ=255)                                          aaaaaGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGc                                                                                                        >  2:720126/1‑150 (MQ=255)                                            aaaGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGTCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGcac                                                                                                      >  1:33647/1‑150 (MQ=255)                                             aaGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCacac                                                                                                    >  2:138672/1‑151 (MQ=255)                                                cGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACAcc                                                                                                   >  2:589152/1‑149 (MQ=255)                                                  ttCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTCCCCGCCCCCTGGTCGCGCGGCAGTTTATAAATATTCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGc                                                                                                <  2:195161/150‑1 (MQ=255)                                                   tCGGTGATTTTTTCCCTTTCGACTCCAAGCGAGACGTTTTTCCCCGCCCCCTGGTCGCGCGGCAGGTTATGAATTTTCTGTCCATGCAGGAAAAAC‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCt                                                                                               <  2:195052/150‑1 (MQ=255)                                                   gcGGTGATATTTCCCCTTCCGCCTTCAAGCGAGAGGTTATGCCCCGGCCCCGGGTCCCGCGGCGGTTAATAAATATTCTGTTCAGGCAGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCa                                                                                                  <  2:195567/146‑1 (MQ=255)                                                         atatTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGa                                                                                         >  2:326829/1‑150 (MQ=255)                                                                             aaGGGAGAGGTTATCCCCCGCCCCCTGGCCGCGCGGAAGGTTATAAATATTCTTTTCAGGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcaca                                                                    <  1:66285/151‑1 (MQ=255)                                                                             aaGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGcac                                                                     >  2:319435/1‑150 (MQ=255)                                                                                 gagaCGGTATTCCCCGGCCCCGGGCCGCGGGGCAGTTTATGAATTTTCTGTTCAGGAGGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCt                                                                         <  1:788190/142‑1 (MQ=255)                                                                                      ggTATTCCCCGGCCCCTGGCCGCGCGGCAGTTTATGATTATTTTTTTCATGGAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcg                                                           <  1:421643/151‑1 (MQ=255)                                                                                      ggTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcg                                                           >  1:788622/1‑151 (MQ=255)                                                                                       gTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCcgc                                                          >  1:381341/1‑151 (MQ=255)                                                                                            ccccGCCCCCGGGTCGCGCGGCAGGTTATAAATTTTTTGTTCAGGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGtt                                                               <  1:734595/140‑1 (MQ=255)                                                                                              ccGCCCCCTGGTCCCCCGGCGGGTTATG‑ATTTTTTTTTCAAGGAAGGAAAAACCCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCg                                                     <  1:635599/149‑1 (MQ=255)                                                                                                    ccggggcgcgggGCAGTTTAAAAATTTTCTGTACATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTg                                             <  2:781150/145‑1 (MQ=255)                                                                                                             gcgGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGtt                                    >  2:589538/1‑151 (MQ=255)                                                                                                                 cAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAAc                                >  2:722144/1‑151 (MQ=255)                                                                                                                     ttATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATg                            >  1:99407/1‑151 (MQ=255)                                                                                                                      tataAATATTCTGTCCAGGAGGGAAAAAA‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATg                            <  2:129136/150‑1 (MQ=255)                                                                                                                            ttttCTGTTCATGCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCAGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACgg                      <  2:653685/148‑1 (MQ=255)                                                                                                                              ttCTTTTCAGACAGGAAAACC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACggg                     <  1:769631/149‑1 (MQ=255)                                                                                                                              ttCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCg                   >  1:751968/1‑151 (MQ=255)                                                                                                                                 tGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCg                   >  2:153871/1‑148 (MQ=255)                                                                                                                                   ttCATGAAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCga                  <  1:405670/147‑1 (MQ=255)                                                                                                                                   ttCAGGCAGGGAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCgag                 <  2:688213/148‑1 (MQ=255)                                                                                                                                        gCAGGAAAAAC‑CCCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCgaga                <  1:589505/144‑1 (MQ=255)                                                                                                                                           gggAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGc      >  2:371595/1‑151 (MQ=255)                                                                                                                                                aaa‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGccacc  >  2:570121/1‑150 (MQ=255)                                                                                                                                                aaa‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGccacc  >  1:196147/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                                  CCGCAACCACCTCGGCACTGACGCGCTTTTCACCGACGACAAAAAAGCGTTCGGTGATATTTTCACTTTCGACTTCAAGCGAGACGGTATTACCCGGCCCCTGGTCGCGCGGCAGGTTATGAATATTCTGTTCATGCAGGGAAAAA‑CTCCCCGCCAGTGTAGCGATTTCACGCTCAGCAACATGGCGCGGCACACCAGCTAATAGAACTTCTCCACGCATCTGCACAATGTTCCCGCGCTCGCCAAGTTGCAAGGTGTTAAACGATGCCACGGGCGAGACTTCCGTTGCCACC  >  NC_000913/3556060‑3556352

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑