Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,580,634	0	C	T	47.1%	45.4 / 29.3	51	E277K (GAA→AAA)	hsdS	specificity determinant for hsdM and hsdR
Reads supporting (aligned to +/- strand):  ref base C (7/20);  new base T (24/0);  total (31/20)
Fisher's exact test for biased strand distribution p-value = 1.16e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAGCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAAT  >  NC_000913/4580493‑4580783                                                                                                                                               |                                                                                                                                                      gAGCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCt                                                                                                                                                <  1:621634/149‑1 (MQ=255) gAGCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGa                                                                                                                                              <  1:724850/151‑1 (MQ=255)   gCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑TACttttttaa                                                                                                                                             >  2:1038422/1‑145 (MQ=255)       gAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTc                                                                                                                                        <  2:450802/151‑1 (MQ=255)        aaTAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCt                                                                                                                                       <  1:304276/151‑1 (MQ=255)           aaGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAAAAtt                                                                                                                                         >  1:135940/1‑146 (MQ=255)           aaGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGa                                                                                                                                    <  1:616041/151‑1 (MQ=255)               ttATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑TACTTTTTGAAAATTCTAGaaa                                                                                                                                  >  2:734139/1‑149 (MQ=255)                tATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTGAAAATTTTATaaaac                                                                                                                                >  1:486871/1‑148 (MQ=255)                   cAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCGTGTAAATTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAat                                                                                                                            <  1:478431/151‑1 (MQ=255)                     ggATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAACATTTTAGAAACCGaa                                                                                                                             >  1:480849/1‑148 (MQ=255)                      gATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAACATTCCCCAAAACGAat                                                                                                                            >  2:832812/1‑148 (MQ=255)                         ataGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGGT‑TACCTTCTTAAAATTCTTGAAACCGCATATCggt                                                                                                                      >  2:427232/1‑149 (MQ=255)                          taGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTTTT‑TACTTTCTGAACATTTTTGAAACCGAATATTGttt                                                                                                                     >  1:1008671/1‑151 (MQ=255)                              aaaTTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGAt                                                                                                                 <  1:850263/151‑1 (MQ=255)                                aTTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TAATTTTTTAAAAATTTTGAAAACGAATATTGTTTTTAttt                                                                                                               >  1:297650/1‑149 (MQ=255)                                  tttGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTa                                                                                                              <  1:894299/150‑1 (MQ=255)                                     gATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACAt                                                                                                           <  2:907295/150‑1 (MQ=255)                                     gATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAAAATTCTAGAAAACGCATATCGTTTTTTTCTACAtt                                                                                                          >  2:398140/1‑150 (MQ=255)                                            tAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑TACTTTTTTAAAATTTTAAAAAACGAATATCGTTTTTTTTTACATTGCCAGc                                                                                                    >  2:1016193/1‑150 (MQ=255)                                             aaTTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑TACTTTCTTAACATTCTAGAAACCGAATATCGTTTTTATCTACATGGcc                                                                                                       >  2:807741/1‑146 (MQ=255)                                             aaTTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCAc                                                                                                  <  1:1061443/151‑1 (MQ=255)                                                 ttttCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAAAATTTTAGAAAACGAATATCGTTTTGTTTTACATTGCCAGCACGt                                                                                                >  1:718564/1‑149 (MQ=255)                                                  tttCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTAc                                                                                              <  2:922103/150‑1 (MQ=255)                                                     cAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑TACTTTTTGAAAAATCTAGAAAACCAATATTGGTTTTTTTTACATTGCCCACACGTACAGa                                                                                           >  1:83210/1‑150 (MQ=255)                                                      aaTAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTTCCCCTTTTTGAA‑ATTCTAAAAAACGAAAATTCTTTTTTTCTTTAAGGCCAggcaccgccaaa                                                                                          >  2:531190/1‑139 (MQ=255)                                                      aaTAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGGT‑TACTTTCTGAAAAATCTTGAAAACGAATATCAGTTTGTTCTACATGGCGCGCACGTACAGaa                                                                                          >  2:752281/1‑150 (MQ=255)                                                         aaCCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAACATTTTAAAAAACGAATATAGGTTTTTTCTTCATTGCCAACACGTaaaaaaata                                                                                       >  1:331539/1‑142 (MQ=255)                                                           cccACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAACATTCTAGAAACCGAATATCGTTTTGTTTTTCATGGCCAGCACGTACAGAAATaa                                                                                      >  2:800556/1‑149 (MQ=255)                                                               caAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTTAT‑TCCTTTCTGAACATTTTATAAAACGAAAATTGTTTTTTTCTACATTGCCCGACCGTACAGAACTAATTCgt                                                                                 >  1:729214/1‑150 (MQ=255)                                                                aaaCACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTTTT‑TACTTTTTTAACATTTTATAAAACCAATATTGTTTTGATTTTCATTGCCAGCCCCTAAAAAAATAATGAgt                                                                                 >  1:39797/1‑149 (MQ=255)                                                                   cacCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑CACTTTCTGAACATTCTAGAAAACGAATATCGTTTTTATCTACATGGCCAGCACGTACAGAACTAATGCgtagta                                                                             >  2:361163/1‑150 (MQ=255)                                                                              tCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCa                                                                  <  1:253649/150‑1 (MQ=255)                                                                                 aaaCTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAaca                                                               <  1:781644/150‑1 (MQ=255)                                                                                       ccGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAACATTCTTGAAAACGAATATTGTTTTTTTTTACATTGCCCGCACGTACAAAAATAATGCGGAGTATTTGATGACCAAAACCACctt                                                        >  1:181627/1‑151 (MQ=255)                                                                                          ttATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑TAATTTCTTAACATTCTAGAAACCGAAAATCGTTTTTATCTACAATGCCCGCACGTACAGAAATAATGCGTAGTATTGGATGAACAACAACACttt                                                        >  2:735497/1‑148 (MQ=255)                                                                                           tataGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGGT‑TACTTTTTTAAAATTTTAGAAAACGAATATTTTTTTTTTTTTCATGGCCCGCCCGTACAAAAATAAAGCGTAGTATTGGGTGAACAACACCACttttctt                                                    >  1:769566/1‑147 (MQ=255)                                                                                                 gAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑TACTTTTTTAACATTCTTGAAAACAAATATCGTTTTTTTCTACATTGCCCGCACGTACAGAAATAATGAGTAGTATTTGATGACCAACACCACCTTCCTTTTGCtt                                              >  1:28853/1‑151 (MQ=255)                                                                                                     aaataaaAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCCAATATCGTTTTTATCTACATGGCCAGCACGTACAGAAATAATGCGTAGTATTGGATGACCAACACCACTTTCATTTTGCTTtgat                                          >  2:43057/1‑151 (MQ=255)                                                                                                        taaaAGATCTCCATCTTGTAATTTGTGGCGGTTTAGGT‑TACTTTCTGAACATTCTAAGAAACGAATATCGTTTTGATTTACATGTCCCGCCCGTACAAAACTAATGCGTAGGATTTGATGACCAACAACCCATTCAATTTGCTTtgatg                                         >  2:119067/1‑149 (MQ=255)                                                                                                           aaGATCTCCATCTTGTAATTTGTGGCGGTTTTGTT‑CACTTTTTTAACATTTTTAAAAACGAATATTGTTTTTTTTTAAATGGCCCGCACCGACAGAAATAATGTGTAGTATTTGATGACCAAAACCACTTTTTTTTTGGTTTTATTaaa                                      >  1:103889/1‑149 (MQ=255)                                                                                                                  ccATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTa                              <  1:633674/150‑1 (MQ=255)                                                                                                                  ccATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTAc                             <  1:694227/151‑1 (MQ=255)                                                                                                                     tCTTGTAATTTGTGGCGGTTTTGTT‑TTCTTTTTGAACATTCTAGAAACCGAATATAGTTTTTATCTACATTGCCAGCACGTACAAAAATAAAACGTAGTATTTGATGAACCAAACCACTTTTATTTTGCTTTGATGAAAGACCAtt                               >  1:881945/1‑146 (MQ=255)                                                                                                                        tGTAATTTGTGGCGGTTTTGTT‑CACTTTTTTGACATTCTTGAAAACGAATATTGTTTTTATTTACATGGCCAGCACGTACAGAAATAAAGCGTAAGATTTGATGAACCACACCACTTTCATTTTGGTTTTATGGAAAAACATTACGTaaat                       >  1:905844/1‑149 (MQ=255)                                                                                                                        tGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTa                          <  2:280535/148‑1 (MQ=255)                                                                                                                                gtgGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAag               <  1:767763/151‑1 (MQ=255)                                                                                                                                    cGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAagatag           <  1:1016171/151‑1 (MQ=255)                                                                                                                                     ggTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAagataga          <  1:173703/151‑1 (MQ=255)                                                                                                                                     ggTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAagat             >  2:972654/1‑148 (MQ=255)                                                                                                                                             t‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCaaaa   <  2:973476/150‑1 (MQ=255)                                                                                                                                               cACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAAt  <  1:948896/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                      GAGCTCGAATAAGTTTATCAGGATATAGCAAATTTTGATGTTGTAATTTTTTCAATAACCCACAAACACCAACAAATTCTAAACTTCCGTTATAGCGAGTAAATAAAAGATCTCCATCTTGTAATTTGTGGCGGTTTAGTT‑CACTTTCTGAACATTCTAGAAACCGAATATCGTTTTGATCTACATGGCCAGCACGTACAGAACTAATGCGTAGTATTGGATGACCAACACCACTTTCATTTGGCTTTGATGAAAGACCATTACGTAATTCAGTTAAGATAGATTCAAAAT  >  NC_000913/4580493‑4580783

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑