Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	U00096	1,708,709	0	T	A	20.8%	75.1 / 22.1	61	R597R (CGT→CGA)	rsxC	SoxR [2Fe‑2S] reducing system protein RsxC
Reads supporting (aligned to +/- strand):  ref base T (14/28);  new base A (6/5);  total (20/41)
Fisher's exact test for biased strand distribution p-value = 2.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.68e-01
Rejected as consensus: Frequency below/above cutoff threshold.

CAGCAACCGTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAAC  >  U00096/1708561‑1708833                                                                                                                                                     |                                                                                                                             cagcaACCGTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGt                                                                                                                              <  1:1427685/149‑1 (MQ=255)   gcaACCGTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGTCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGACGAAGCAGATATTGCCCGTGc                                                                                                                            >  2:1427762/1‑149 (MQ=17)     aaCCGTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCGAAAGGAAAATGCTCAAGCAGAAAAACAGGTCGAAACGCGCAAAGCCCCCGTCGAAGACGCTAAAGCCCGTGCCa                                                                                                                          >  2:1427816/1‑149 (MQ=17)        cGTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGAGCCAAAGCGCGCAAGCTGGAACAGCACCAAACAAATGCGTATACAGAAAAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAg                                                                                                                       >  2:1427764/1‑149 (MQ=17)         gTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAgc                                                                                                                      <  1:1427687/149‑1 (MQ=255)         gTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAgc                                                                                                                      <  1:1427688/149‑1 (MQ=255)          ttGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGGCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAgc                                                                                                                      <  1:1427689/148‑1 (MQ=255)           tGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAgcgc                                                                                                                    <  1:1427690/149‑1 (MQ=255)           tGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAgcgc                                                                                                                    <  1:1427691/149‑1 (MQ=255)              tGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATACTCGCAAAGCCGCCGTCGAAGCCTCTATTGCCAGTGCCAAAGCGCGCa                                                                                                                 >  2:1427694/1‑149 (MQ=255)                  ccACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCt                                                                                                             <  2:1427695/149‑1 (MQ=255)                   cACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTg                                                                                                            <  2:1427696/149‑1 (MQ=255)                    aCGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTgg                                                                                                           <  2:1427697/149‑1 (MQ=255)                       tAAAACTGCAGTTGAAGAAGCTATCTCCCGCGACAAATCGCGCAAGCTGGAACATCAACAGGATAATTCGGAACCAGAACAACAGGTCGATCCGCGAAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAAc                                                                                                        <  2:1427698/149‑1 (MQ=17)                        aaaaCTGCCGTTTCTGCAGCTATCGCCTGCGCCTAAGCTCGCAATCTGGAACATCATCAGGCTAATTCGGAACCAGAACAAGAGGCCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACa                                                                                                       <  2:1427699/149‑1 (MQ=14)                            cTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCaa                                                                                                   <  2:1427700/149‑1 (MQ=255)                            cTGCAGTTGATGCAGCTATCTCCCGCGCCAAATCGCGCAATCTGGAACAGCATCAGGCTAATGCGGAACCAGAACAAGAGGTCGATCCGCGAAAAGCAGCCGTCGAAGCAGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCaa                                                                                                   <  2:1427702/149‑1 (MQ=14)                             tGCCGTTGAAGCAGCTATCGCCCGCGCCAACGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACCACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAAc                                                                                                  <  1:1427704/149‑1 (MQ=255)                              gCCGTTGAAGCAGCTATCGACCGCGCCAAAGCTCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCTCGCAAAGCCGCCGTCGAAGCAGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACa                                                                                                 <  2:1427705/149‑1 (MQ=255)                                   tGACGCAGCTATCGACCGGGCCACATCCCGCAAGCTGGAAGAGCTTCATGCTACTGCGGCAGCAGCACAAGAGGCGGAGCCGCGGAAACCTGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTa                                                                                            <  2:1427742/149‑1 (MQ=9)                                                 acctcgcgAAAGCGCTCAAGCAGGAACATCATCAGGCTACTCAGGACGCAGCACCAGAGGCCGATCCTCGTAAATCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCagaa                                                                              <  2:1427741/145‑1 (MQ=9)                                                     ctgcAAAGCGCGCAAGCTGGAACAGCTACAGTCTAATGCGGAAACAGAACAACATGTCTATCCTCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAAc                                                                          <  1:2622052/146‑1 (MQ=14)                                                      gcCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCaaa                                                                                                                        >  2:1427781/1‑102 (MQ=17)                                                         aaaGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCaaa                                                                                                                        >  2:1427784/1‑99 (MQ=18)                                                         aaaGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCaaa                                                                                                                        <  1:1427784/99‑1 (MQ=18)                                                             cgcgcAAGCTGGAACAGCAACAGGCTAATGCGGATCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCa                                                                                                                          <  2:1427785/93‑1 (MQ=12)                                                             cgcgcAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCa                                                                                                                          >  1:1427785/1‑93 (MQ=18)                                                                gcAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTgg                                                                                                           <  1:1427713/105‑1 (MQ=35)                                                                  aaGCTGGCAGACCATCAGGCAAATGACGACCCAGCACCCCTGGGCGATCCTCGCAAATCCGCCGTCGAAGCCGCTATTTCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCcgcg                                                             <  1:1427728/149‑1 (MQ=14)                                                                    gCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGCCAAAGCGCGCaa                                                                                                                >  1:1427792/1‑96 (MQ=18)                                                                     cTGGAACAGCATCAGGATAATCCGGACGCAGAACACCAGGGCGATCCGCGAAAAGCCGCCGTCGAAGCAGCTATTGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCaa                                                          <  1:1427715/149‑1 (MQ=14)                                                                          aCAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAgccg                                                     <  1:1427717/149‑1 (MQ=255)                                                                                aCAGGCTAATTCGGTACCACCACATCTTGCCGATCCTCGCAAATCTGCCGTCGAAGCAGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCg                                               <  2:1427729/149‑1 (MQ=14)                                                                                 cAGGCTAATCAGGACCCAGCACCACATGCCGATCCTCGCAAACCCGCCGTCGAAGCCGCTATTGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGa                                              <  2:1427731/149‑1 (MQ=14)                                                                                     atacttaggAAGCAGAAAAAGTTGTCGATCCTCGCAAACCCGCCGTTGAAGCAGCTTTAGCCCGAGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGcc                                          <  2:1427725/142‑1 (MQ=11)                                                                                       aaTGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCt                                                                                             >  1:1427753/1‑96 (MQ=37)                                                                                       aaTGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGcc                                                                                                                           >  2:1427798/1‑66 (MQ=25)                                                                                       aaTGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGcc                                                                                                                           >  2:1427799/1‑66 (MQ=25)                                                                                       aaTGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGcc                                                                                                                           <  1:1427799/66‑1 (MQ=25)                                                                                       aaTGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGAGcc                                                                                                                           <  1:1427798/66‑1 (MQ=25)                                                                                              aaCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGCACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGcc                                 >  2:2010044/1‑149 (MQ=255)                                                                                               aCCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGccc                                <  2:1427723/149‑1 (MQ=255)                                                                                                       accaGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCaaa                        <  2:1427724/147‑1 (MQ=255)                                                                                                          aGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCTCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCa                                                                                 >  2:1427874/1‑89 (MQ=255)                                                                                                               gATCCTCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAg                                                                        <  1:1427735/93‑1 (MQ=255)                                                                                                               gATCCTCGCAAACCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAgg                                                                       <  1:1427734/94‑1 (MQ=255)                                                                                                               gATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGa                                                                                     <  1:1757741/80‑1 (MQ=39)                                                                                                               gATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACa                                                                         <  1:1427737/92‑1 (MQ=255)                                                                                                                     ccccaacccgccgccgAAGCCCCTATCGCCCGCGTCAAAGCTATCTAGATGGTACAGCAACCTGCTAAACAGTAAACAGAACCACCTCTCGATCCGCTCATATCTGCCGTTGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGa          <  2:1427772/142‑1 (MQ=2)                                                                                                                       ccaccccgccgTCGAAGCCGCTATCGCCCGCGCCAAATTTCTAAAGCTTTAAGTGGAACAGGGTTATGTTGAACCATAACAACATGGCGTCGCTTGCTAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAAc        <  2:1427768/144‑1 (MQ=2)                                                                                                                        accgccgccCTCGAAGCCGCTATCGCCCGCGCCAAAGCGCGCAAGCTTTAACTGCAACTGGCTAATGCGGAACCAGAAGAACAGGTCTATCCTCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACa       <  2:1427738/146‑1 (MQ=11)                                                                                                                        aaaGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACa       <  1:2693607/149‑1 (MQ=255)                                                                                                                          cccccccgccgAAGCCGCTCTCGCCCGCGCCAACGCGCTCTAGCTGTAACTGCAACGGGCTAATGCGGAACCACAACACCATGCCGATCCGCGCATCTCCGCAGCCGAAGCCGCTATTGCCCGCGCCAAAGCACGCAAGCTGGAACAGc     <  2:1427744/144‑1 (MQ=9)                                                                                                                            ccgccgTCGAAGCCGCTATTGCCCGTGCCAAAgcgcgc                                                                                                                  >  1:1427810/1‑38 (MQ=40)                                                                                                                             cgccgTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCAGAAGAACAGGTAGATCCGCGCAAAGCAGCCGTCGAAGCCGCTATTGCACGAGCCAAAGCACGCAAGCTGGAACAGCagc  >  2:1427828/1‑147 (MQ=11)                                                                                                                                    gAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGc                                                                                              >  1:1427893/1‑50 (MQ=38)                                                                                                                                     aaGCCGCTATTGCCCGGGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGt                                                                      <  1:1427746/73‑1 (MQ=255)                                                                                                                                       gCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACCGGCTAATGc                                                                                        >  1:1427826/1‑53 (MQ=255)                                                                                                                                       gCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAGCCaga                                                                               >  1:1427821/1‑62 (MQ=255)                                                                                                                                         cGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATc                                                                 >  1:1427747/1‑74 (MQ=255)                                                                                                                                           cTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAAc                                                                          >  1:1427907/1‑63 (MQ=255)                                                                                                                                           cTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGTACCAGAAGAAc                                                                          <  2:1427907/63‑1 (MQ=255)                                                                                                                                                     |                                                                                                                             CAGCAACCGTTGCTGATCCACGTAAAACTGCCGTTGAAGCAGCTATCGCCCGCGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAACAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCGCGCAAGCTGGAACAGCAACAGGCTAATGCGGAACCAGAAGAACAGGTCGATCCGCGCAAAGCCGCCGTCGAAGCCGCTATTGCCCGTGCCAAAGCACGCAAGCTGGAACAGCAAC  >  U00096/1708561‑1708833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑