Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,864,099	0	C	A	47.7%	46.2 / 26.3	44	R67R (CGC→CGA)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (18/5);  new base A (1/20);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 5.30e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCAACG  >  NC_000913/3863958‑3864247                                                                                                                                              |                                                                                                                                                     gCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGt                                                                                                                                              >  2:593994/1‑150 (MQ=255)               ttcCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGc                                                                                                                               >  1:677111/1‑151 (MQ=255)                     gtaaaaaaaaGCGGGCGAAAGATTTGGCGGTATCGGGGATGACCATCCGTAAACCCATTGCCCTGCTGGTGGGGGGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTCCTCCATCAAACCGCCAGTCt                                                                                                                         <  2:225995/148‑1 (MQ=255)                       gAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTg                                                                                                                        >  1:31827/1‑150 (MQ=255)                          aaatcgCTGACGGGAGTGTCTGCGGTATCACGGACGACCATCCGTAAAGCCATTGACCTGCTGGGCGCGTGGCAGCTGGTGGTCTGCTGCCACGGTCGTCGCCTTCATCTGGTGGGACAAGATGTACTGCAACAAACCCCCCGTCTTAc                                                                                                                      >  2:429713/6‑149 (MQ=255)                            aaaGCGGGGGGAAGAGTTTGCGGTATCGCGGATGCCCATCCGTAAAGCCATTGCCCTGCTGGTGGGGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCggg                                                                                                                  <  1:628354/151‑1 (MQ=255)                               gCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtg                                                                                                               >  2:699594/1‑151 (MQ=255)                                 tGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtgg                                                                                                              >  2:780583/1‑150 (MQ=255)                                  ggCGAAAGAGTTTGGGGTACCGGGGAGAACAACCGGGAAGGCAATGGCCCTGGGGGTGGCGGGGGGGCGGGGGGTCCGCCGCCACGGTGGGGGCTCTTCCCGGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCtggtg                                                                                                            <  2:540437/151‑1 (MQ=255)                                   gCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtggtgg                                                                                                           >  1:235582/1‑151 (MQ=255)                                        agagTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGgtg                                                                                                      >  2:308905/1‑151 (MQ=255)                                                 gttaccgcgGATGACCATCCGTAAAGCCATTGCCCTGTGGGTAGCGTGGGGGCGGGTGGTCCCCCGCCACGGTAGTGCCCCTTCCCTGGTGCGCAAAAATGTACTCCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACg                                                                                              <  1:614103/145‑1 (MQ=255)                                                 ggTACCGGGGATGACCATCCGTAAATCCATTGCCCTGCTGGTGGGGGGGGGGCTGGTGGTCCCCCCCCACGGTAGTGCCACTTCCCTGGCGCGAAAAGATGTACTGCATCAACCCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACgg                                                                                             <  1:681424/151‑1 (MQ=255)                                                   tATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGc                                                                                            >  1:41156/1‑150 (MQ=255)                                                    aTCGGGGATGACCTTCCGTAAAGCCTTTGCCCTGCTGGTAGGGTGGGGGCGGGTGGTCCGCCCCCAGGGTAGTGGCACTTCCCGGGTGCGAAAAGATTTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCa                                                                                           <  1:537330/150‑1 (MQ=255)                                                        cgGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGa                                                                                       >  1:609615/1‑150 (MQ=255)                                                         ggaggcccATCCGAAAGGCCATTGACCTGCTGGTGGGGTGGGGGCTGGTGTCCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGAAACAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaa                                                                                     <  1:20305/145‑1 (MQ=255)                                                         ggATGACCATCGGAAAAGCCTTTGCCCGGCTGGTAGCGGGGGGGCGGGGGGCCCGCCGCCACGGTAGGGGCACTTCCCGGGTGCGAAAAGATTTACTGCAACAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaa                                                                                     <  2:442385/151‑1 (MQ=255)                                                               ccATCCGAAAAGCCATTGCCCTGCGGGTAGCGGGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGt                                                                               <  1:500333/151‑1 (MQ=255)                                                                    cGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAcc                                                                           >  1:328552/1‑150 (MQ=255)                                                                       aaaGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcc                                                                       >  2:720494/1‑151 (MQ=255)                                                                        aaGCCATGGCCCTGCGGGTGGCGGGGGGGGTGGGGGTCCCCCCCCACGGTAGTGCCATTTCCGGGGGGCACAAAGATGTACGGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcca                                                                      <  2:289173/151‑1 (MQ=255)                                                                           cctttGCCCTGTTGGTAGCGTGGGGGTTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCGGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagccag                                                                     <  1:402274/146‑1 (MQ=255)                                                                           ccATTGACCGGCTGGTAGCGTGGGGGCTGGTGCTCCCCCGCCAGGGTAGTCGCCCTGACCTGGTGCGAAAAGATGTACTCCATCAACCCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGt                                                                   <  1:654428/151‑1 (MQ=255)                                                                             aTTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGTAAAACGGTCAccagcc                                                                       >  2:401428/1‑145 (MQ=255)                                                                                 cccTGTTGGTGGGGTGGGGGCTGGTGGCCCGCCGCCAGGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGAt                                                             <  2:568224/150‑1 (MQ=255)                                                                                  ccTGCTGGTGGGGGGGGGGCGGGGGGCCCGCCGCCAGGGTAGGGGCACTTACCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCt                                                                <  1:427483/147‑1 (MQ=255)                                                                                      ctgGTGGCGGGGGGGGTGGTGGGCCGCCGCCACGGTAGTGGCTCTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGAttt                                                           <  1:734123/148‑1 (MQ=255)                                                                                          tAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAAt                                                    >  1:77201/1‑151 (MQ=255)                                                                                              gggggggTGGGTGGTCGGCCGCAACGTGAGTGGCCCTACCCTGGTGCAAAAAGATGTTCTGAATTAACCCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATc                                                   <  1:464341/146‑1 (MQ=255)                                                                                                gggggCTGGTGGTCGGCCGCCTCGGTAGTGGGCCTTGCCTGGTGGGCAAAGAGTTTCTACATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGcc                                              <  1:576854/151‑1 (MQ=255)                                                                                                       ggtggtCCGCCGCCACGGTGGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGcc                                        <  2:203746/150‑1 (MQ=255)                                                                                                          ggtCCGCCGCCACGGTGGTGGCATTTCCCGGGTGCGAAAAGATGTACTGCAACAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTgcg                                          <  2:54266/145‑1 (MQ=255)                                                                                                           gtCCGCCGCCCGGGTGGTGGCACTTCCCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTc                                      <  2:767470/148‑1 (MQ=255)                                                                                                             ccccccccaggggggTGGCCCTTCCCTGGTGCGAAAGGAGGTACTGCACCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTcc                                     <  2:19575/133‑1 (MQ=255)                                                                                                               gccgccACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCAt                               >  1:246858/1‑151 (MQ=255)                                                                                                                 cgccACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTg                             >  2:61977/1‑151 (MQ=255)                                                                                                                 cgccACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTACGCCTCCGGCCATTg                             >  1:480974/1‑151 (MQ=255)                                                                                                                       ggTAGTGGCCTTTCCCTGGTGCGAAAAGATGTACTGCACAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccag                         <  2:517316/149‑1 (MQ=255)                                                                                                                        gTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccagcc                       >  1:369473/1‑150 (MQ=255)                                                                                                                         tggTGGCCCTTCCCGGGTGCGAAAAGATGTACTGCACAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccagcca                      <  2:760230/148‑1 (MQ=255)                                                                                                                         tAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccagcc                       >  1:41038/1‑149 (MQ=255)                                                                                                                                        ggTGCGAAAAGATTTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAAt       <  2:208536/150‑1 (MQ=255)                                                                                                                                        ggTGCGAAAAGAGGTACTGCACAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTc           <  2:578821/146‑1 (MQ=255)                                                                                                                                             gcAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCAACg  >  2:276943/1‑150 (MQ=255)                                                                                                                                              cAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCAACg  >  1:769405/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                                     GCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCAACG  >  NC_000913/3863958‑3864247

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑