Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,984,441	0	A	C	43.6%	95.1 / 14.8	56	G384G (GGT→GGG)	yqeF	short chain acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (28/3);  new base C (1/23);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 3.04e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTGACCC  >  NC_000913/2984298‑2984586                                                                                                                                                 |                                                                                                                                                   gTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑Gc                                                                                                                                            <  2:1029681/151‑1 (MQ=255)       agaATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCccgc                                                                                                                                      <  2:355139/151‑1 (MQ=255)            ggAAAAATGAGGGAGCCCAGAAAATGTATATCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGAt                                                                                                                                  >  1:106303/1‑150 (MQ=255)                aaaTGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACaa                                                                                                                              >  2:726313/1‑150 (MQ=255)                    gAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGt                                                                                                                         >  2:1003007/1‑151 (MQ=255)                     aGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGtt                                                                                                                        >  1:901985/1‑151 (MQ=255)                        gAGCCCAGAAAATGTATGTCGGCTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGACATGCAGAGCTATTAGTCACGTTCAATGGTCA‑ATACTACACCCTG‑GCCCCCGCCGATACAAAGCGTTGcc                                                                                                                     >  2:753351/1‑151 (MQ=255)                            ccAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTc                                                                                                                 >  2:256035/1‑151 (MQ=255)                              aaaaaaTGTATGTCGCCTTGCCACCCTTAATTATTCAACAAATTAATGCCGGCAAATTTTTACGGGTAAGGAGAAAATGCAGAGTTATTCGTCACGTTAAATGTTAA‑ATGCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTc                                                                                                                 <  2:956604/147‑1 (MQ=255)                              aaaaaaGGTATGTCATGTTGCAAACCATAATTATTCAAAAGAAGAATGAGGGCAGATATTTAACGGTAAGGAGGAAAGACAGAATTATTGGTCATG‑TCAATTGTCAGAATCCGCGCCTTG‑CCCACCGCCGATACAAAGCGTTGCCAGTCCt                                                                                                               <  1:830668/149‑1 (MQ=255)                               gAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCtt                                                                                                              >  2:673481/1‑151 (MQ=255)                                            gACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACg                                                                                                 >  1:506609/1‑151 (MQ=255)                                            gACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACg                                                                                                 >  2:339882/1‑151 (MQ=255)                                               ttGCCAGCCTTCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGCGTAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCAACCACCTG‑GCCCCCGCCGAGACAAACCGTTTCCACTCCTTTGCGGGCATTACGtt                                                                                               >  2:178917/1‑150 (MQ=255)                                                 gccagcctTCTTTATTCAACAGATGAAGGCCGGCAGATATTTATCGTAAAGGAGAAAAGGGGGAGCTTTTCGTCCCTTTCAATGTTAA‑AGCCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACg                                                                                                 <  1:917259/146‑1 (MQ=255)                                                  ccagactTCATTATTCAACAAATAAATGCCGGAAGATTTTAAGCGGTAAGGAGAAAATGAAGAGTTTTTCGTCCCTTTAAATGGTAA‑ACGCCACCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCAtt                                                                                                    <  2:807277/142‑1 (MQ=255)                                                      ccaTCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAtt                                                                                       >  1:340254/1‑151 (MQ=255)                                                      ccaTCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAtt                                                                                       >  1:545594/1‑151 (MQ=255)                                                      ccaTCATTATCCAACAGATTAATGACGGCAAATATTTAGCGGTAGGGAGAAAAGGCAGACCTTTTCGCCACTTTCAGTGGTCA‑ATCCCCCCCCCGG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAt                                                                                        <  2:501361/150‑1 (MQ=255)                                                      cacttttttttCAACAGATTAATGAGGGTAGATTTTTGTCGGTAGGGAGTAAAGGCAGAGCTATTCGTCAGTTCCATTGGTAA‑ATGCCACACCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAtt                                                                                       <  1:286563/142‑1 (MQ=255)                                                            ttattaAACAGATTAAGGACGGAAAATTTTTAGGGGTAAGGAGAAAATGCAGAGTTTTTCGTCACTTTAAATGTTCA‑ATCCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCAt                                                                                        <  1:729094/144‑1 (MQ=255)                                                            ttattaAACAAATTAATGACGGCAGATTTTTATGGGAAAGGAGGAAATGCAGACCTATTCGTCAGGTTAAATGTCCA‑ATCCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCa                                                                                            <  2:1036018/140‑1 (MQ=255)                                                                tCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAAcc                                                                              >  2:958456/1‑150 (MQ=255)                                                                  aaaaaaTTAATGACGGCAGATATTTATCGGAAAGGAGGAAATGCAGAGTTTTTCGTCACGTTAAATGGTCA‑ATCCCACCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCaga                                                                           <  1:811088/146‑1 (MQ=255)                                                                     aGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAgaga                                                                         >  2:71418/1‑150 (MQ=255)                                                                         tAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAAcc                                                                     >  1:648753/1‑150 (MQ=255)                                                                         tAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAAcc                                                                     >  2:326913/1‑150 (MQ=255)                                                                             gACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGAt                                                                >  2:122176/1‑151 (MQ=255)                                                                             gACGGCAGATATTTATCGGTAAGGAGAAAATGCAGAGTTATTCGTCCCGTTAAATGGTCA‑ATGCCACCCCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGa                                                                 <  1:792613/150‑1 (MQ=255)                                                                              aCGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGAtt                                                               >  2:134811/1‑151 (MQ=255)                                                                               cGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTc                                                              >  1:633488/1‑151 (MQ=255)                                                                                ggCAGATTTTTACGGGTAAGGAGAAAATGCAGAGCTTTTCGTAACTTTAAATGGTCA‑ATGCCCCCCCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTc                                                              <  2:923455/150‑1 (MQ=255)                                                                                   aGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGc                                                           >  1:445215/1‑150 (MQ=255)                                                                                    gttttttACCGGAAAGGAGAAAATGAAGAGCTATTCGTCACGTTAAATGGTCA‑ATCCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGAt                                                                <  2:886763/140‑1 (MQ=255)                                                                                      tttttAGCGGAAAGGAGAAAATGCAGAGTTTTTCGTCACGTTCAATGGCAA‑AGCCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAAc                                                        <  1:185137/148‑1 (MQ=255)                                                                                      tatTTAGGGGTAAGGAGGAAATGCGGAGTTATTCGTCACGTGCAATGGTAA‑ATCCCCCCCCCGG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAAc                                                        <  2:71030/150‑1 (MQ=255)                                                                                        tttATCGGTAAGGAGGAAATGCAGAGCTTTTCGTCACTTTCAATGGTCA‑ATCCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCg                                                      <  1:845816/150‑1 (MQ=255)                                                                                        tttATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCgg                                                     >  1:513650/1‑151 (MQ=255)                                                                                        tttATCGGAAGGGAGGAAATGGAGATCTTTTGTTCACTTACAATGGTCA‑ATCCCCCCCCCGG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAAc                                                        <  1:907581/148‑1 (MQ=255)                                                                                         ttaggggTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCgg                                                     <  2:507148/145‑1 (MQ=255)                                                                                             cGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAgcg                                                >  1:747776/1‑151 (MQ=255)                                                                                               gaagggggaaaaTGCTGATTTTTTCGTCACTTTAAAGGGT‑A‑ATGCCCCCCCCCGCGCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGaa                                                   <  1:247712/137‑1 (MQ=255)                                                                                                 aaGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCt                                             >  1:524141/1‑150 (MQ=255)                                                                                                    gaggaAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCg                                         >  2:237611/1‑151 (MQ=255)                                                                                                      ggaAATGCAGAGCTTTTCGTCGGGTTCAATTGTCA‑GTGCCACCCCCGG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCg                                         <  1:962425/149‑1 (MQ=255)                                                                                                       aaaaTGAAGATCTTTTCAACCCTTTAAATGGACA‑ATCCCACCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGt                                      <  2:945141/150‑1 (MQ=255)                                                                                                             cAGATCTATTCGCCACTTTCAAAGGTCA‑ATCCCACCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCg                                 <  1:46990/150‑1 (MQ=255)                                                                                                                agtttttggTCACGTTAAATGGTAA‑AGCCCCCCCCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGAcc                                  <  1:627631/138‑1 (MQ=255)                                                                                                                    tttCGTCACTTTCAATGGTCA‑ATGCCCCCCCCTG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAg                               <  2:316988/144‑1 (MQ=255)                                                                                                                     ttCGTCACTTTAAATGGTAA‑ACCCCACCCCCGG‑CCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGAt                         <  2:479173/150‑1 (MQ=255)                                                                                                                      tCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATcg                       >  2:480613/1‑151 (MQ=255)                                                                                                                        gTCACGTTCAATGGTCA‑ATGCCACCCCCGG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATcg                       <  1:872907/149‑1 (MQ=255)                                                                                                                            cGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGccac                 >  2:932020/1‑151 (MQ=255)                                                                                                                             gTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGccacc                >  2:20329/1‑151 (MQ=255)                                                                                                                                       cA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACcattgacattg      >  2:725211/1‑151 (MQ=255)                                                                                                                                            gCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTGAccc  >  1:672028/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                   GTCATGAGAATGGAAAAATGAGGGAGCCCAGAAAATGTATGTCGACTTGCCAGCCATCATTATTCAACAGATTAATGACGGCAGATATTTATCGGTAAGGAGGAAATGCAGAGCTATTCGTCACGTTCAATGGTCA‑ATGCCACACCCTG‑GCCCCCGCCGATACAAAGCGTTGCCAGTCCTTTGCGGGCATTACGTTTCACCATTTCATGAACCAGAGAAACCAGGATTCGGCAACCGGAAGCGCCTATCGGGTGACCGAGTGCGATCGCGCCACCATTGACATTGACCC  >  NC_000913/2984298‑2984586

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑