Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,825,056	0	G	A	42.2%	67.0 / 21.1	45	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 (25/1);  new base A (0/19);  total (25/20)
Fisher's exact test for biased strand distribution p-value = 8.20e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAA  >  NC_000913/1824911‑1825203                                                                                                                                                    |                                                                                                                                                     cATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGagaaa                                                                                                                                                   >  2:889091/1‑149 (MQ=255)  aTTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGagaaa                                                                                                                                                   >  1:1069436/1‑148 (MQ=255)     ttACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGagaaaag‑aaa                                                                                                                                             >  2:392069/1‑150 (MQ=255)      tACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAAc                                                                                                                                           >  2:934791/1‑151 (MQ=255)      tACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAAc                                                                                                                                           >  2:568532/1‑151 (MQ=255)      tACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGCGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAAc                                                                                                                                           >  2:1182348/1‑151 (MQ=255)        cGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAAccg                                                                                                                                         <  2:322126/151‑1 (MQ=255)        cGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAAcc                                                                                                                                          >  2:1105099/1‑150 (MQ=255)          cATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAAccgcc                                                                                                                                       >  1:695928/1‑151 (MQ=255)             atCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGAt                                                                                                                                    >  1:1066561/1‑151 (MQ=255)               cAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATcc                                                                                                                                  >  1:944233/1‑151 (MQ=255)                    tATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTcc                                                                                                                             >  2:73531/1‑151 (MQ=255)                           tccTCGCTCCGGCCCCTTTTTTTTAATTTTTATCGTTCAGGAACCCGTGGATGTTTCCCGCCAGCGGGGTTTATTTACTTTAGGGGTGATCGGGTTTTTTTTACAAC‑TGTTGA‑AGAAAAAAAAAA‑AAAACCGCCGATCCTGTCCAcc                                                                                                                          <  2:332099/145‑1 (MQ=255)                                 cTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGc                                                                                                                >  1:1153754/1‑151 (MQ=255)                                  tCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGc                                                                                                                >  1:706821/1‑150 (MQ=255)                                   cccGGCCCTTTCTTTTCTTTTTTATCGTTCAGGTACCCGTGGATGTTTATCGGCAACTGGGGTGATTTACGTTAGTGGTGATCAGGTTTTTTTTACAAT‑TTTTTG‑AGAAGAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCa                                                                                                               <  2:935575/150‑1 (MQ=255)                                      gccccTTTTTTTTTTTTTTTATCTTTCGGGTAACGGGGGTTGTTTATCGGCACCTGGGGTATTTTACTTTAGGGGTGACCGGGTTTTTTTTACACT‑TGTTTA‑AGAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAg                                                                                                             <  2:405370/147‑1 (MQ=255)                                         ccGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGt                                                                                                        >  1:113595/1‑151 (MQ=255)                                            ttCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTgg                                                                                                      >  2:57282/1‑150 (MQ=255)                                              cTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGAc                                                                                                    >  2:193893/1‑150 (MQ=255)                                               ttttCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACa                                                                                                   >  1:1142290/1‑150 (MQ=255)                                                         tATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACcggcgg                                                                                         >  1:291420/1‑150 (MQ=255)                                                             gTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCtt                                                                                     >  1:504948/1‑150 (MQ=255)                                                                 agttatcggTGGTTGTTTACCGGCATCTGGGGTGTTTTACGTTAGTGGTGACCTTTCTTTTTTAACAAT‑GGTTTG‑AGAAGAAAAAAA‑AAAGCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGtt                                                                                <  2:1057719/143‑1 (MQ=255)                                                                 aGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGAGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAggt                                                                                >  1:560294/1‑149 (MQ=255)                                                                    tAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGttttt                                                                             >  1:361649/1‑151 (MQ=255)                                                                           gggtgtttATCGACACCTGGGGTTTTTTAGGTTAGTGTTGATCAGTTTTTTTTTACACT‑TTTTTG‑AGAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTg                                                                           <  1:650529/140‑1 (MQ=255)                                                                             aTGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGaa                                                                     >  2:1003987/1‑150 (MQ=255)                                                                                 ttATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGatt                                                                >  2:550183/1‑151 (MQ=255)                                                                                         acctggggTGTTTTACGTTAGTGGTGATAAGGTTTTTTTTACAAC‑TGTTTG‑AAAAGAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTcagca                                                        <  2:373430/146‑1 (MQ=255)                                                                                             cGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGtt                                                     >  1:979688/1‑150 (MQ=255)                                                                                              gggTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGtt                                                     >  1:262830/1‑149 (MQ=255)                                                                                                    tttcctttagggtggATCAGTTTTTTTTAAAAAC‑TGTTGA‑AGAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAg                                                 <  1:15744/133‑1 (MQ=255)                                                                                                    tttACGTTAGGGGTGATCAGGTTTTTTTTACATC‑TTTTGG‑AAAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCa                                                  <  1:405695/146‑1 (MQ=255)                                                                                                          ttgggggtgATCAGGTTTTTTTTAAACC‑TGTTGG‑AAAAGAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTa                                         <  1:12206/144‑1 (MQ=255)                                                                                                          ttAGTGGTGATCAGTTTTTTTTTACAAC‑TGTTGG‑AAAAGAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCAtttt                                          <  1:376780/148‑1 (MQ=255)                                                                                                            aggggttatcggcttttttttCCACC‑TGTTAA‑AAAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCAtttt                                          <  2:1059521/132‑1 (MQ=255)                                                                                                             gtggtgATCGGTTTTTTTTTACAAC‑TTTTGG‑AGAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCt                                      <  1:577246/149‑1 (MQ=255)                                                                                                             gtggtgATCAGTTTTTTTTTACATC‑TTTTGG‑AAAAGAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCttt                                    <  1:515335/151‑1 (MQ=255)                                                                                                                ggtaatcggttttttttACCACTTGTTTG‑AGAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCt                                      <  1:568530/137‑1 (MQ=255)                                                                                                                 tgATCGGGTTTTTTTTACAAT‑TTTTGG‑AAAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTg                                  <  1:264295/149‑1 (MQ=255)                                                                                                                     cAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTTGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGc                              >  1:434152/1‑149 (MQ=255)                                                                                                                         ttttttttACATT‑TTTTGG‑AAAAGAAAAAAA‑AAATCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGAc                         <  2:317219/149‑1 (MQ=255)                                                                                                                           ttttttAACAC‑TTTTTGAAAAAAAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGAc                         <  2:975841/149‑1 (MQ=255)                                                                                                                               ttACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGt                  >  1:975598/1‑151 (MQ=255)                                                                                                                                   aaC‑TTTTGG‑AAAAGAAAAAAA‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAg               <  1:392068/150‑1 (MQ=255)                                                                                                                                       tGTTTG‑AGAAGAAAAAAA‑AAACCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACg            <  1:354166/150‑1 (MQ=255)                                                                                                                                          ttG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCCGGACGGTCTGTCAGACGCtt         >  2:1085534/1‑150 (MQ=255)                                                                                                                                                 agaaaaaagaaaaaCCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCa     <  1:217104/149‑1 (MQ=255)                                                                                                                                                  gagaaAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCaaaa  >  1:1092367/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CATTTTACGCATATCAAAGTATTCCATACTCGCTCCCGGCCCGTTCTTTTCATTGTTATCGTTCAGGTAACCGTGGATGGTTATCGGCAACTCGGGTGATTTACGTTAGTGGTGATCAGGCTTTTTTTACAAC‑TGTTTG‑AGAAGAGAAAAG‑AAAACCGCCGATCCTGTCCACCGCATTACTGCAAGGTAGTGGACAAGACCGGCGGTCTTAAGTTTTTTGGCTGAAAGATTATTCAGCAGTTGCAGGCATTTTACCTTTTGCCGCTGGACGTTCTGTCAGACGCTTCTCAAAA  >  NC_000913/1824911‑1825203

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑