Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,764,785	0	T	A	44.0%	60.3 / 27.1	51	intergenic (‑399/+149)	sufA/ydiH	Fe‑S cluster assembly protein/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (23/5);  new base A (0/22);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 9.87e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGAGATAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATTAAGTC  >  NC_000913/1764638‑1764929                                                                                                                                                    |                                                                                                                                                  aaGAGATAGGTAAAAAAGGGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATaa                                                                                                                                                 >  1:393728/1‑150 (MQ=255)       tAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑c                                                                                                                                         >  1:641909/1‑151 (MQ=255)            aaaaaaGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTATCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑Cccgcc                                                                                                                                    >  1:833206/1‑151 (MQ=255)                     cAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAac                                                                                                                            >  1:627091/1‑150 (MQ=255)                     cAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAac                                                                                                                            >  1:479973/1‑150 (MQ=255)                             aaaaaaaaaaaaCCCCTTAAGTCTGTGCGACACGGGCTTAGGGTTTTCTCCCCCACCCGGCGCTTATCCCCGCCCCTCTCGGTGGTTTAGCTCTGGAGGGGGCGAAAAAAATAATCTAAAAAAGCTAC‑CCCGCCGTTTTAACACAAACTg                                                                                                                    <  1:495743/148‑1 (MQ=255)                             aaaaaaaaaaaaCCCCTAAAGTCTGGGCACCACAGGTTTAGGGTTTCCTCCCCCACCGGGCCTTTATCCCCGCCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAAAAAAATCTAAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGc                                                                                                                   <  2:907015/149‑1 (MQ=255)                                  tAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGAtt                                                                                                               >  2:648152/1‑150 (MQ=255)                                         aCCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGtattat                                                                                                       >  2:781460/1‑151 (MQ=255)                                             ttAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTAttttt                                                                                                   >  2:468766/1‑151 (MQ=255)                                                 gTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAAc                                                                                               >  2:400182/1‑151 (MQ=255)                                                  tCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAAc                                                                                               >  2:435632/1‑150 (MQ=255)                                                     gtgcaccacaGGTTTAGGGTTTCCCCCCCCACCCGGCTCTTTTCCCCGCCCCTCTCAGTGGCTTAGCTTTTGAAGGGGAAATAAAAATAATCTAAAAAAGCAAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAata                                                                                           <  2:30057/145‑1 (MQ=255)                                                     gtgCGACACGGGCTTAGGGTTTTCTCCCCCACCCGGCGCTTATCCCCGGCCCTCTCAGTGGTTTAGCTCTTGAAGGGGAGATAAAAATAATCTAAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAAc                                                                                               <  1:657126/147‑1 (MQ=255)                                                     gtgCGACACAGTTTTAAGGTTTCCCCCCCCACCGGGCCCTTATCCCCGGCCCTCACAGTGGCTTAGCTTTTGAAGGGGCAATAAAAATAACCTAAAAAACCAAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACa                                                                                              <  1:270449/148‑1 (MQ=255)                                                         gACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATc                                                                                         >  1:848907/1‑149 (MQ=255)                                                             caGGCTTAAGGTTTTCTCCCCCACCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCAATAAGAATAATCTCAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCg                                                                                    <  1:382787/150‑1 (MQ=255)                                                                      gggTTCCTACCCCACCCGGCGCTTATCCCCGGCTCTGCGAGTGGTTTTCCGCTTAAGGGGGCGAAAAGAATAATCTAATAAAGTAAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATa                                                                             <  1:1023251/148‑1 (MQ=255)                                                                       ggTTTCCACCCCCTCGGCCCTTTATCCCGGACCTTCTCAGTGCCTTAGTCTTTAAAGGGGGAAAAAAAATATGCTAAAAAATTTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCa                                                                         <  1:320516/151‑1 (MQ=255)                                                                         tttcccccccACCCGGCGTTTATCCCCGCCCCTCTCAGTGGCTTAGCTTTTAAAGGGGAGAAAAAAATAATCAAAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAg                                                                        <  2:461414/144‑1 (MQ=255)                                                                          ttCTCCCCCACCCGGCTCTTATCCCCGGCACTCTAAGTGGTTTAGCTTTTGAAGGGGCGATAAGAATAATCTAAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGt                                                                       <  1:806681/150‑1 (MQ=255)                                                                          ttCTCCCCCACCCGGCGTTTATCCCCGGCCCTCTCAGGGGCTTAGCTCTTGAGGGGGCGATAAAAATAATCTAAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGt                                                                       <  1:1030891/150‑1 (MQ=255)                                                                              cccccACCCGGCGTTTATCTCCGGCCCCCTCAGTGGTTTCGCTCTTGAAGGGGCGAAAAAAATAATCCAAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTaa                                                                  <  1:516896/150‑1 (MQ=255)                                                                               ccccACCCGGCGCTTATCCCCGGCACTCTCAGTGGCTTAGCTTTTGAAGGGGCAATAAAAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTAtt                                                                    <  1:994678/148‑1 (MQ=255)                                                                                  cATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTaaga                                                                >  1:49768/1‑149 (MQ=255)                                                                                  cATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTaaga                                                                >  1:408827/1‑149 (MQ=255)                                                                                  cATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTaaga                                                                >  2:417940/1‑149 (MQ=255)                                                                                            ttATCTCCGGCCCTCTCGGTGGTTTAGCTCTAGAAGGGGCAATAAAAATAATCTAAAAAAGCAAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGa                                                      <  2:641719/149‑1 (MQ=255)                                                                                            ttATCTCCGGCACTCTCAGTGGTTTAGCTCTTGAAGGGGCGATAAGAATAATCTCAAAAAGCTAC‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGaa                                                     <  1:975941/150‑1 (MQ=255)                                                                                                  ccGCCACTCTCAGTGGCTTAGCTTTTGAAGGGGAAAAAAAAATAATCTAAAAAAGAAAC‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGa                                               <  2:184669/150‑1 (MQ=255)                                                                                                    ggCCCTCTCAGTGGCTTAGCTTTTGAGGGGGCAATAAGAAAAATCGCAAAAAGCTAC‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGa                                               <  1:112077/148‑1 (MQ=255)                                                                                                      cACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACgg                                            >  2:387687/1‑149 (MQ=255)                                                                                                       aCTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAgg                                         >  2:858661/1‑151 (MQ=255)                                                                                                       aCTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAgg                                         >  1:428466/1‑151 (MQ=255)                                                                                                            cAGTGGCTTAGCTCTTGAGGGGGCAAAAAGAATATTCTCAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTa                                      <  1:47291/149‑1 (MQ=255)                                                                                                             aGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATc                                   >  1:51799/1‑151 (MQ=255)                                                                                                               tGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATcc                                  >  1:94098/1‑150 (MQ=255)                                                                                                                   ttAGTTTTTGAGGGGGCAATAAAAATAATCTCAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAgg                               <  1:1015107/149‑1 (MQ=255)                                                                                                                    ttgctttggAAGGGGGAAAAAGAAAATTATCA‑AAAACTAACCCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAg                                <  1:549957/139‑1 (MQ=255)                                                                                                                     aGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCg                            >  2:944920/1‑150 (MQ=255)                                                                                                                             aaGGGGCGAAAAGAATAATCTCATAAAGCAAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGAttt                        <  1:692282/146‑1 (MQ=255)                                                                                                                              atgggCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGa                   >  1:6535/3‑150 (MQ=255)                                                                                                                               gggtcaaaaaaaataatCTAAAAAAGCAAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCg                    <  2:305309/137‑1 (MQ=255)                                                                                                                               gggggtaTAAAAATAATCTCAAAAAGTAAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGa                   <  2:924109/143‑1 (MQ=255)                                                                                                                               ggggggATAAAAATAATCAAAAAAAGCTAC‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGaa                  <  1:218436/150‑1 (MQ=255)                                                                                                                                     aaaaGAAAAATCTAATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCg            <  1:298671/148‑1 (MQ=255)                                                                                                                                       aaGAATAATCTAATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCg            <  1:857045/148‑1 (MQ=255)                                                                                                                                          aataatCTAAAAAATCAAC‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATTa      <  2:52195/151‑1 (MQ=255)                                                                                                                                          aaaaatCTAAAAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATTa      <  1:81374/148‑1 (MQ=255)                                                                                                                                             aatCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATTAAGt   >  2:827745/1‑151 (MQ=255)                                                                                                                                               tctcATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATTAAGTc  >  2:935640/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                  AAGAGATAGGTAAAAAAGTGCAGCGTTCAGAAATAAGAAAACCCTTAAGTCTGTGCGACACAGGCTTAAGGGTTTCTACCCCATCCGGCGCTTATCTCCGGCACTCTCAGTGGCTTAGCTCTTGAAGGGGCGATAAGAATAATCTCATAAAGCTAA‑CCCGCCGTTTTAACACAAACTGCGATTAGTATTATTTTTGAACAATATCAGGCGGTAGATAAGCAGTATTAAGAAGGTCATCGAACCTGGACGGAGGTTAATCCAGGTCGATTTGGCGAACTTGCGGCATTAAGTC  >  NC_000913/1764638‑1764929

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑