Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	543,207	0	A	T	20.0%	107.3 / 20.1	45	intergenic (+174/+54)	glxK/allE	glycerate kinase II/S‑ureidoglycine aminohydrolase
Reads supporting (aligned to +/- strand):  ref base A (21/15);  new base T (2/7);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 7.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

TCCTTCCTGAAAATCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTACAATCTTTCGAGTAAATATA  >  NC_000913/543111‑543302                                                                                                 |                                                                                                tccttcctGAAAATCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATaa                                                                                              >  1:683974/1‑100 (MQ=255)      cctGAAAATCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGt                                                                                         >  1:647690/1‑100 (MQ=255)         gAAAATCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGc                                                                                      >  1:1105871/1‑100 (MQ=255)          aaaaTCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTTTATACCGTGGct                                                                                     <  2:1071798/100‑2 (MQ=255)           aaaTCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTTTATACCGTGGctt                                                                                    <  2:599746/100‑3 (MQ=255)             aTCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTTTATACCGTGGctttt                                                                                  <  1:825966/100‑5 (MQ=25)              tCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTCAC‑AAAAAAGCCACGGTTTATACCGTGGctttttt                                                                                <  1:928894/100‑7 (MQ=21)               cgcgCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTTTATACCGTGGctttttt                                                                                <  2:885210/100‑7 (MQ=25)               cgcgCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTTTATACCGTGGctttttt                                                                                <  2:543730/100‑7 (MQ=25)               cgcgCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTTTATACCGTGGctttttt                                                                                <  1:1005532/100‑7 (MQ=25)               cgcgCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATc                                                                                >  2:350925/1‑100 (MQ=255)                gcgcAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATcn                                                                               <  2:711989/100‑2 (MQ=255)                 cgcAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCa                                                                              >  2:544789/1‑100 (MQ=255)                   cAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAAc                                                                            <  2:964985/100‑1 (MQ=255)                    aaaTTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACa                                                                           >  2:1098236/1‑100 (MQ=255)                    aaaTTATATATATTGCAGAGATCATATAGACATAATAAGCGAAGCGCATAAGTCAATATTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATc                                                                                <  2:827974/95‑1 (MQ=25)                        tCTATATATTGCAGAAATCATGTAAGCCTGATAAGCGAAGCGCATCAGGAAAAAAAAAAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGc                                                                       <  2:493234/100‑1 (MQ=21)                         cTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCt                                                                      >  2:982107/1‑100 (MQ=255)                           atatatTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTaa                                                                    >  1:299125/1‑100 (MQ=255)                              tatTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTaaaaa                                                                 >  2:716581/1‑100 (MQ=255)                              tatTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTaaaaa                                                                 >  1:494918/1‑100 (MQ=255)                                ttGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAaata                                                               >  1:833447/1‑100 (MQ=255)                                ttGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAaata                                                               >  2:32532/1‑100 (MQ=255)                                  gCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAaataat                                                             >  1:979463/1‑100 (MQ=255)                                  gCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAaataat                                                             >  2:309884/1‑100 (MQ=255)                                             gTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTgg                                                  >  1:729398/1‑100 (MQ=255)                                              tAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGt                                                 <  1:1045415/100‑1 (MQ=255)                                               aGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTa                                                <  1:692404/100‑1 (MQ=255)                                                ggCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTAt                                               >  2:38768/1‑100 (MQ=255)                                                 gCCTGATAAGCGAAGCACATCAGGCAATATTACAAAAAAAGCCACGGTATAAACCGTGGCAATATCCAACATAGCTAAAAATAATCAGTCGAGTGGTAt                                               <  2:645347/99‑1 (MQ=39)                                                     gATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACtt                                          >  2:1010808/1‑100 (MQ=255)                                                      aTAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTa                                         <  2:1216675/100‑1 (MQ=255)                                                          gcgaagcgCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAAtc                                     <  2:683970/100‑1 (MQ=255)                                                          gcgaagcgCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAAtc                                     <  1:782604/100‑1 (MQ=255)                                                            gaagcgCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAAtctc                                   <  2:494914/100‑1 (MQ=255)                                                            gaagcgCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTACGACTTAAAtctc                                   <  1:858856/100‑1 (MQ=255)                                                             aagcgCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATctct                                  <  1:318453/100‑1 (MQ=255)                                                                  cATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTc                             >  1:69770/1‑100 (MQ=255)                                                                      aGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCgg                         >  2:906012/1‑100 (MQ=255)                                                                         cAATGTTACAAAAAAAGCCACGGTATAAATCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTa                      >  2:830290/1‑100 (MQ=255)                                                                                  ggattttgCCACGGTTTATACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTACAATCTTTc             >  1:1230442/8‑100 (MQ=39)                                                                                   aaaaaaGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTACAATCTTTCg            >  1:201340/1‑100 (MQ=255)                                                                                    attttgCCACGGTTTATACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTACAATCTTTCGa           >  2:960518/6‑100 (MQ=255)                                                                                    aaaaaGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTACAATCTTTCGa           <  2:929478/100‑1 (MQ=255)                                                                                               gTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTACAATCTTTCGAGTAAAtata  <  1:618315/98‑1 (MQ=255)                                                                                                 |                                                                                                TCCTTCCTGAAAATCGCGCAAATTCTATATATTGCAGAGATCATGTAGGCCTGATAAGCGAAGCGCATCAGGCAATGTTACAAAAAAAGCCACGGTATAAACCGTGGCAAAATCCAACATAGCTAAAAATAATCAGGCGAGTGGTATGACTTAAATCTCTACGTCGCGGTTACAATCTTTCGAGTAAATATA  >  NC_000913/543111‑543302

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑