Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,177,748	0	C	A	40.0%	54.8 / 27.5	50	E55* (GAG→TAG)	nudF	ADP‑ribose pyrophosphatase
Reads supporting (aligned to +/- strand):  ref base C (22/8);  new base A (0/20);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 1.26e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGG  >  NC_000913/3177598‑3177889                                                                                                                                                        |                                                                                                                                              cacTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGACAAGGGGTTTCGCTGGCGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCTCGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTc                                                                                                                                               <  1:565734/151‑1 (MQ=255)    tttCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTAAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCaa                                                                                                                                             >  2:512653/1‑150 (MQ=255)        aCCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAAtt                                                                                                                                        >  1:765792/1‑151 (MQ=255)               tCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCccg                                                                                                                                   <  2:745443/149‑1 (MQ=255)                cAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGGAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTcac                                                                                                                                    >  2:157129/1‑145 (MQ=255)                 aaTCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCcgccgc                                                                                                                               >  2:472759/1‑151 (MQ=255)                  atcatcCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCcgccgc                                                                                                                               >  1:349376/1‑150 (MQ=255)                             acccATCCCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGa                                                                                                                      <  1:373637/146‑1 (MQ=255)                                cATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCAtt                                                                                                                >  1:525067/1‑151 (MQ=255)                                   ctcCAGTAGCCAGGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCAAAACTTCACCCCGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCAtt                                                                                                                <  2:393636/148‑1 (MQ=255)                                     ccgatAGCCGAGGGTTTTCGCGGGGGTCGTCGGCGGAAATCCGAATCTCCGCAACCACCCCACCTCCATCGCGCA‑TGGGTGAAAAGGGAAGAAAAAGTGCGGGGTGACCGCCCGAAAAAATTTCCCGCCGCACCTCATGACTCATTTg                                                                                                              <  2:371498/144‑1 (MQ=255)                                     ccAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAACGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGccc                                                                                                           >  2:582958/1‑151 (MQ=255)                                     ccAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAACCTGCTCAACCACCACACCTTCATCCCCCACTGGGT‑CAAAGGGTACCAAGCCTGCGGCGTGCCCGCGCAAAAAAATTTCCCGCCGCACCTCATGACTCATTTGccc                                                                                                           <  2:631453/151‑1 (MQ=255)                                                 ggttttCGCTGGTGTCGTCCGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGAAAGACTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACg                                                                                               <  1:486507/148‑1 (MQ=255)                                                 gggTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACg                                                                                               >  1:162693/1‑151 (MQ=255)                                                 gggTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACg                                                                                               >  2:178508/1‑151 (MQ=255)                                                  gttttCGCTGGTGTCGTACGCGGAAACCGAAACCTGCTCAATCAGCACAACTTCACCCCGCCCTGGGT‑CAAAGGGTGGCAAGACTGCGGCGTGCCCGCTCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGa                                                                                              <  2:489292/149‑1 (MQ=255)                                                    tttCGCGGGGGTCTTACGCGGCAATCCGAATCTGCACAACCAGCACACTTCCATCGCGCCCTGGGT‑CAAGGGTTAGCAAGACTGCGCCGTGCCCGCGATAAAAAATTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGa                                                                                              <  2:427882/149‑1 (MQ=255)                                                     ttCGCTGGTGTCGTACGCGCCAATCCGAATCTGCTCAATCAACACAACTCCACCACGCCCGGGGT‑AAAAGGGTAGAAAGACTCCGGCGTGCCCGCGCCCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATg                                                                                            <  1:472821/150‑1 (MQ=255)                                                        gCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACg                                                                                         >  1:222208/1‑150 (MQ=255)                                                          tGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGaa                                                                                       >  2:181458/1‑150 (MQ=255)                                                          tGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCCCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGaa                                                                                       >  2:25763/1‑150 (MQ=255)                                                            gtgttatACGCGGCAATCCGAACCTGCTAAATCACCCCATCTTCATCACACACTGGGT‑CAAAGGGTGACAAGACTGCGGTGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATc                                                                                    <  1:212049/145‑1 (MQ=255)                                                                cGTACGGGGAAATCCAAATCTCCTAAATCAGCCAAACTGCAGCACGCACGGGGT‑CAAAGGGTAGCAAGCCTGGGGCGTGACCGCGCGAAAAAATTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCtat                                                                                 <  1:689287/150‑1 (MQ=255)                                                                    cgcgGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATaa                                                                               >  1:3211/1‑148 (MQ=255)                                                                    cgcgGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATaaa                                                                              <  1:110322/149‑1 (MQ=255)                                                                      cgGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATaa                                                                               >  2:243112/1‑146 (MQ=255)                                                                       ggCAATCCGAATCTGCTCAATCAGCACAACTTCACCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGAt                                                                           <  1:407469/149‑1 (MQ=255)                                                                       ggCAATCCGAATCTGCTCAACCAGCACACCTTCATCCCGCACGGGGT‑CAAAGGTTAGCAAGACTGCGGCGTGACCGCCCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATc                                                                          <  1:471635/150‑1 (MQ=255)                                                                          aaTCCAAATCTCCTCAATCAGCACAACTTCAACACGCACTGGGT‑AAAAGGGTAGCAAGCCTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTa                                                                        <  1:682569/149‑1 (MQ=255)                                                                             ccGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCAGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGaa                                                                   <  1:411529/151‑1 (MQ=255)                                                                             ccGAATCTGCTCAATCAGCACAACTCCACCCCGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGaa                                                                   <  1:558978/151‑1 (MQ=255)                                                                              cGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGaa                                                                   >  1:316446/1‑150 (MQ=255)                                                                               gAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGaaa                                                                  >  1:616541/1‑150 (MQ=255)                                                                                aaTCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGaaaa                                                                 >  1:186430/1‑150 (MQ=255)                                                                                    tGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGc                                                            >  1:497997/1‑151 (MQ=255)                                                                                                acaACTTCATCCCTCACTGGGT‑CAAAGGGTAGCAAGACGGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAgtg                                                <  2:402751/151‑1 (MQ=255)                                                                                                        atcgCGCACGGGGT‑CAAAGGGTAGCAAGCCGGCGGCGTGCCCCCGCTAAAAATTTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACTATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTtct                                           <  1:193217/148‑1 (MQ=255)                                                                                                              cACTGGGT‑CAAAGGGTAGCAAGCCTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCaata                                  <  2:203228/151‑1 (MQ=255)                                                                                                                  gggT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTAAAAAATTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAAttt                              <  2:578338/151‑1 (MQ=255)                                                                                                                  gggT‑CAAAGGGTAGCAAGACGGCGGCGTGCCCCCCCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAAttt                              <  1:629120/151‑1 (MQ=255)                                                                                                                  gggT‑CAAAGGGTAGAAAGACTGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTg                                       <  2:100265/142‑1 (MQ=255)                                                                                                                  gggT‑AAAGGGGTAGAAAGCCGGCGGCGGGCCCGCGTTAAAAAATTGCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAAtt                               <  1:380201/150‑1 (MQ=255)                                                                                                                  gggA‑CAAGGGGTAGCAAGCCGGCGGCGTGACCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAAttt                              <  2:719181/151‑1 (MQ=255)                                                                                                                    gccaaaggggTACAAAGACTGGGGCGTGCCCGCGCTAAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTc                             <  2:525002/144‑1 (MQ=255)                                                                                                                        aaaGGGTAGCAAGACTGCGGCGTGACCGCCCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCt                            <  1:737161/148‑1 (MQ=255)                                                                                                                                  aataCTGCGGGTTGCCCGCGCTAAAAAATTCCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGttttt                 <  2:23016/146‑1 (MQ=255)                                                                                                                                   aGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGcc              >  1:287845/1‑151 (MQ=255)                                                                                                                                     aCTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCa             >  2:38470/1‑150 (MQ=255)                                                                                                                                         cggcgTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATg         >  1:578734/1‑150 (MQ=255)                                                                                                                                                 tctcgcTCAAAAATTGTTCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGGTCTAATGACAAAAAACCGCGATAAAGTGTTTCTCGTGCCATATTTTCTACATCGTTTTTGCCAAATGTAACggg  >  2:23992/4‑149 (MQ=255)                                                                                                                                                        |                                                                                                                                              CACTTTCACCCTCTTCAATCATCCCGGCAACCATCTCCAGTAGCCAAGGGGTTTCGCTGGTGTCGTACGCGGCAATCCGAATCTGCTCAATCAGCACAACTTCATCACGCACTGGGT‑CAAAGGGTAGCAAGACTGCGGCGTGACCGCGCTCAAAAATTTCCCGCCGCACCTCATGACTCATTTGCCCGTTGAATAGACGATGACGAAATCTATAAAGATCTAATGAAAAAAAGCCGCGATAAAGTGTTTCTCGTGCAATAATTTCTACATCGTTTTTGCCAAATGTAACGGG  >  NC_000913/3177598‑3177889

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: ‑