Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,825,056	0	G	A	45.6%	46.0 / 28.5	46	intergenic (‑119/+84)	ves/spy	cold‑ and stress‑inducible protein/periplasmic ATP‑independent protein refolding chaperone, stress‑induced
Reads supporting (aligned to +/- strand):  ref base G (21/4);  new base A (0/21);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 1.90e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAA  >  NC_000913/1824910‑1825203                                                                                                                                                      |                                                                                                                                                    aCATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGagaaaa                                                                                                                                                 <  1:716447/151‑1 (MQ=255) aCATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGagaaa                                                                                                                                                  >  2:74180/1‑150 (MQ=255)     tttACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGagaaaagaa                                                                                                                                              <  2:188679/150‑1 (MQ=255)         cGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAAccg                                                                                                                                         <  1:256581/151‑1 (MQ=255)         cGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAAccg                                                                                                                                         <  2:145863/151‑1 (MQ=255)                          cATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGATCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGCAAACCGCCGATCCTGTCCACCGc                                                                                                                        >  2:105912/1‑151 (MQ=255)                             aCTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCAtt                                                                                                                     >  1:423993/1‑151 (MQ=255)                              cTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCAtt                                                                                                                     >  2:756774/1‑150 (MQ=255)                              cTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCAtt                                                                                                                     >  2:37879/1‑150 (MQ=255)                                cGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACt                                                                                                                  >  1:357783/1‑151 (MQ=255)                                    cgcgaccggTTTTTTTCATTGTTTCTGTGCAGGTTGCCGTGGATGCTTAGCGG‑AAGCCGGGTTACTTTCAGTTGGTGTTG‑TGATGCTTTTCTTAAAAATTGTTGG‑GCAAGAAAAAAGGAAACCGCCGATCCTGTCCACCGCAtt                                                                                                                     <  1:199770/136‑1 (MQ=255)                                      cGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAgg                                                                                                            >  1:155167/1‑151 (MQ=255)                                         cccGTTCTTTTCATTGTTATCGTTCAGTTACCCGTGTATGTTTATCGGCAACTGGGGTAA‑TTTACGTTAGTGGTAACCAGGTTTTT‑TTTACATCTTTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTa                                                                                                          <  2:21859/150‑1 (MQ=255)                                          ccGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGt                                                                                                        >  2:393475/1‑151 (MQ=255)                                           cGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTg                                                                                                       >  1:432978/1‑151 (MQ=255)                                           cGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTg                                                                                                       >  1:570349/1‑151 (MQ=255)                                                         ttATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcggagg                                                                                         >  1:523742/1‑151 (MQ=255)                                                           aTCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcggcgg                                                                                         >  1:338863/1‑149 (MQ=255)                                                              gtgcagttagcggtgggtggTTAGCGGCACCTGGGGTAA‑TTTACGGTAGTCGTGATATGTTTTTT‑TTAACAAGTGGTGG‑AGAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCtt                                                                                     <  1:774878/138‑1 (MQ=255)                                                              gTTCAGGTAACCGTGGATGTTTATCGGCACCTCGGGTGA‑TTTACGTTAGTGGTGATCAGGTTTTT‑TTTACAATTGTTTG‑AGAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCtt                                                                                     <  1:30964/150‑1 (MQ=255)                                                                      aaCCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGtttttt                                                                            >  1:363032/1‑151 (MQ=255)                                                                      aaCCGGGGGTGGTTACCGGCAACTC‑GGTGATTTTTAGTTAGGGGTAATC‑GGCTTTT‑TTTTCCACTTTTTGAAAAAAAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGtttttt                                                                            <  2:486605/151‑1 (MQ=255)                                                                        cggTGGATGTTTATCGGCACCTGGGGTAA‑TTTACTTTAGTGGTGATCAGGTTTTT‑TTTACAACTGTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTg                                                                           <  2:152529/148‑1 (MQ=255)                                                                        ccGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTTAGtttttt                                                                            >  2:313043/1‑149 (MQ=255)                                                                            ggttgtttAGCGGCAACGGGGGTAA‑TTTACGTTGGTGGTAATCGGGTTTTT‑TTTACAACTTTTTG‑AAAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTg                                                                       <  2:744835/144‑1 (MQ=255)                                                                                  ttATCGGCAACTGGGGTGA‑TTTACGTTAGGGGTGATCAGGTTTTT‑TTTACAATTTTTAA‑AAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGat                                                                 <  2:377974/150‑1 (MQ=255)                                                                                    accGGCATCGCGGTTGT‑TTTAGGTATGTGGTGATCCGGTTTTT‑TTAAAAACTGTTTG‑AAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGattat                                                              <  1:495700/149‑1 (MQ=255)                                                                                                gggtattttACTTTGGTGGGAATCGGGTTTTT‑TTTACAACTTTTTG‑AAAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTg                                                    <  2:335668/144‑1 (MQ=255)                                                                                                       ttACGTTAGTGGTGATCAGTTTTTT‑TTTACAACTTTTGG‑AGAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCAt                                             <  1:183933/150‑1 (MQ=255)                                                                                                          cGTTAGGGGTAATCAGGTTTTT‑TTTACAACTGTTTG‑AGAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCAtttt                                          <  2:522121/150‑1 (MQ=255)                                                                                                           gTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTa                                         >  2:496300/1‑150 (MQ=255)                                                                                                            ttgttggtgAGCGGTCTTTT‑TTTACAACTGTTAG‑AAAGGAGAAAAAAAAGCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTa                                         <  2:683286/145‑1 (MQ=255)                                                                                                             tAGTGTTGTTCAGTTTTTT‑TTTACCATTGTTTG‑GGAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTa                                         <  2:623440/148‑1 (MQ=255)                                                                                                                gggtgttctgtttttt‑tttACAACTGTTGA‑AGAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCAtttt                                          <  1:469403/132‑1 (MQ=255)                                                                                                                 ggtgATCAGGTTTTT‑TTTACAACTGTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTAcc                                       <  2:155199/146‑1 (MQ=255)                                                                                                                 ggtgATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCtttt                                   >  1:335937/1‑150 (MQ=255)                                                                                                                    gATCGGGTTTTT‑TTTACAATTTTTGG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGcc                                <  1:251535/150‑1 (MQ=255)                                                                                                                       cAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCt                             >  1:619075/1‑150 (MQ=255)                                                                                                                         gtttttt‑tttACAACTGTTGG‑AAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGa                          <  1:74153/148‑1 (MQ=255)                                                                                                                            tttt‑tttACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGt                       >  2:28187/1‑151 (MQ=255)                                                                                                                                 tttCCACCTTTTTA‑AGAAGAGAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCt                    <  1:729764/150‑1 (MQ=255)                                                                                                                                  ttACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGt                  >  2:476315/1‑151 (MQ=255)                                                                                                                                      aaCTTTTTG‑AGAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGt                  <  1:83206/147‑1 (MQ=255)                                                                                                                                      aaCTGTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGt                  <  2:448430/147‑1 (MQ=255)                                                                                                                                       aCTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGATTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGAc             >  2:536111/1‑151 (MQ=255)                                                                                                                                        cTGTTTG‑AGCAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGTAAGATTATTCAGCCGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTTTGTCAGAc             >  1:296769/1‑150 (MQ=255)                                                                                                                                          gTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGACTTAAGTTTTTTTGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGAc             >  1:765578/1‑148 (MQ=255)                                                                                                                                           tttG‑AAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCt          <  1:283461/150‑1 (MQ=255)                                                                                                                                            ttG‑AAAAAAAAAAAAAAATCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCtt         <  2:708461/150‑1 (MQ=255)                                                                                                                                                aaaagagaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCtt         <  2:345030/145‑1 (MQ=255)                                                                                                                                                 gaagagaaAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCa     >  2:347137/1‑150 (MQ=255)                                                                                                                                                   agaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCaaaa  <  2:480971/151‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                    ACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGA‑TTTACGTTAGTGGTGATCAGGCTTTT‑TTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAA  >  NC_000913/1824910‑1825203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑