Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,825,056	0	G	A	43.2%	53.3 / 25.8	44	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 (22/3);  new base A (0/19);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 2.19e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCA  >  NC_000913/1824910‑1825200                                                                                                                                                    |                                                                                                                                                 aCATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGagaaaa                                                                                                                                              <  2:966895/151‑1 (MQ=255) aCATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGagaaaa                                                                                                                                              <  2:656845/151‑1 (MQ=255) aCATTTTACGCATATCAAAGTATT‑CATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGagaaa                                                                                                                                               >  1:178216/1‑149 (MQ=255)        aCGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAAcc                                                                                                                                       <  1:252117/151‑1 (MQ=255)         cGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAAccg                                                                                                                                      >  2:495314/1‑151 (MQ=255)                    gTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGt                                                                                                                            >  2:904227/1‑150 (MQ=255)                      aTTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTcc                                                                                                                          >  2:491575/1‑150 (MQ=255)                        tCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCAcc                                                                                                                       >  1:199723/1‑151 (MQ=255)                        tCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCAcc                                                                                                                       >  1:28251/1‑151 (MQ=255)                            tccTCGCTCCCGCCCTGTTTTTTTCTTTTTTATCGTTCGGGAAACCGTGGATGGTTATCGGCAACTGGGGTGATTTACTTTAGTGGTGATCGGGTTTTTTTTACAACTTTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCAc                                                                                                                        <  1:899314/144‑1 (MQ=255)                            tACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCAt                                                                                                                   >  2:989242/1‑151 (MQ=255)                                  cTCCCGGCCCGTTTTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGTTTTTTTTACAACTGTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTa                                                                                                                 <  1:45149/147‑1 (MQ=255)                                      cGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAgg                                                                                                         >  1:316090/1‑151 (MQ=255)                                            tttcttttcttTGTTTTGTTTCAGGTAACCGTGGATGGTTACCGGCACCTGGGGTGTTTTACGTTAGGGGTGATAAGGTTTTTTTTACACTTGTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAg                                                                                                          <  1:229588/143‑1 (MQ=255)                                             tttttttattttttctCGTTCGGGAAACCGTGGTGGGTTATGGACACCTGGGGTATTTTCCGTTGGGGGTGAACGGGTTTTTTTAACAATTGTTTG‑AGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTgg                                                                                                   <  1:348631/135‑1 (MQ=255)                                                            tCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCt                                                                                   >  1:597139/1‑151 (MQ=255)                                                                       aCCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTg                                                                        >  1:841085/1‑151 (MQ=255)                                                                         cGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTgg                                                                       >  2:414411/1‑150 (MQ=255)                                                                          gTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTgg                                                                       >  1:896333/1‑149 (MQ=255)                                                                            ggATGTTTACCGGCAACTGGGTTGATTTACGTTAGTGGTGATCGGTTTTTTTTTAAAACTGTTGG‑AGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGa                                                                   <  1:158389/151‑1 (MQ=255)                                                                                     tCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGGCTTAAGTTTTTTGGCTGAAAGattatt                                                          >  2:558304/1‑151 (MQ=255)                                                                                      cGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACGACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTTGCTGAAAGattatt                                                          >  2:865672/1‑150 (MQ=255)                                                                                          accgggggTGTTTTACGTTGGTGGTGATCAGGTTTTTTTTACAATTGTTTG‑AAAAGAAAAAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTcagc                                                      <  2:629303/145‑1 (MQ=255)                                                                                          aaCTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTcagca                                                     <  1:31924/151‑1 (MQ=255)                                                                                            cTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTcagc                                                      >  1:217246/1‑148 (MQ=255)                                                                                               gggTGTTTTACGTTAGTGGTGATCGGGTTTTTTTTAAAATTGTTTG‑AAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGtt                                                  <  1:363341/149‑1 (MQ=255)                                                                                               gggTAATTTACTTTATTGGTAATCGGGTTTTTTTTACAATTGTTGA‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTcagca                                                     <  2:761727/146‑1 (MQ=255)                                                                                                    aTTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGc                                            >  1:1004520/1‑150 (MQ=255)                                                                                                     tttACTTTAGGGGTGATCAGGTTTTTTTTACAGCTTTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGc                                            <  1:725629/149‑1 (MQ=255)                                                                                                     tttACGTTGGTGGTGACCAGGTTTTTTTTA‑AACTGTTTGAAAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAgg                                             <  1:989255/148‑1 (MQ=255)                                                                                                      ttcgtttAGTGTTAATGAGGTTTTTTTTACAACTGTGGG‑AAAGGAGAAAAAAACACCGCCGATCCTGTCCACGGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCa                                               <  1:38613/140‑1 (MQ=255)                                                                                                      ttACGTTGGTGGTAATCAGGTTTTTTTTACAATTGTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCAt                                          <  1:43663/150‑1 (MQ=255)                                                                                                        aCGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGGTGCAGGCAtttt                                       >  2:656755/1‑151 (MQ=255)                                                                                                             aGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTTAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCCGGCATTTTACCtt                                  >  2:517074/1‑151 (MQ=255)                                                                                                                gttgATCAGTTTTTTTTAACATTTTTTGA‑AAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCtt                                  <  2:477064/146‑1 (MQ=255)                                                                                                                ggtgATCAGGTTTTTTTTACAATTTTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCtt                                  <  1:170115/148‑1 (MQ=255)                                                                                                                ggtgACCGGCCTTTTTTTAAAATTTTTTA‑AGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCttt                                 <  1:542050/149‑1 (MQ=255)                                                                                                                   gATCAGTTTTTTTTTACAATTGTTTG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTg                               <  2:247594/148‑1 (MQ=255)                                                                                                                   gATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCCTTTTACCTTTTGCCg                            >  1:27164/1‑151 (MQ=255)                                                                                                                    aTCAGTTTTTTTTTAAATGTGTTGG‑AGAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCtttt                                <  2:146423/146‑1 (MQ=255)                                                                                                                        ggttttttttAAAACTTTTGG‑AGAAGAAAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGa                       <  1:148990/148‑1 (MQ=255)                                                                                                                         tttttttttACAACTTTTGA‑AAAAAAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTg                         <  2:1023975/146‑1 (MQ=255)                                                                                                                         gCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGGGGACAAGACCGGCGGTCTTTATTTTTTTTGGTGTAAGAGTATTCAACAGGGGGAGGGGTTTTTACTTTTGCCCCGGGAc                      >  1:48477/1‑151 (MQ=255)                                                                                                                                ttACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTTGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGt               >  2:580238/1‑151 (MQ=255)                                                                                                                                  aCAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTTAGCAGTTTCCGGCATTTTACCTTTTGCCGCTGGACGTTCTGTc              >  1:434790/1‑150 (MQ=255)                                                                                                                                   cagcgtttgg‑agaaaaaaaAAAAAAGCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCt                 <  2:378110/137‑1 (MQ=255)                                                                                                                                     aCTGTTTG‑TGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGCAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGGTTATTCAGCAGTTGCAGGCATTTTCCCTTTTGCCGCTGGACGATCTGGTAGAc          >  2:816635/1‑151 (MQ=255)                                                                                                                                       tGTTGG‑AAAAGAAAAAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGAc          <  1:491581/149‑1 (MQ=255)                                                                                                                                              agaagaaaaAAAAAACCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTtctc   <  2:843112/150‑1 (MQ=255)                                                                                                                                              agaagaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTtct    <  1:589346/149‑1 (MQ=255)                                                                                                                                              agaagaaaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTtc     <  1:495320/148‑1 (MQ=255)                                                                                                                                                aagagaaAAAAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCa  <  2:383874/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                 ACATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAACTGTTTG‑AGAAGAGAAAAGAAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCA  >  NC_000913/1824910‑1825200

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑