Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,621,118	0	A	C	43.8%	53.7 / 14.1	48	V7G (GTG→GGG)	eamA	cysteine and O‑acetyl‑L‑serine efflux system
Reads supporting (aligned to +/- strand):  ref base A (16/11);  new base C (0/21);  total (16/32)
Fisher's exact test for biased strand distribution p-value = 6.44e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.78e-01

TTTCGGTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGATTT  >  NC_000913/1620973‑1621267                                                                                                                                                  |                                                                                                                                                       tttCGGTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCTGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACAcccc                                                                                                                                                    >  2:778949/1‑150 (MQ=255)     ggTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCtt                                                                                                                                               <  2:222692/151‑1 (MQ=255)        cGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCtttt                                                                                                                                             <  2:11448/150‑1 (MQ=255)         gTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTcg                                                                                                                                           >  2:395393/1‑151 (MQ=255)            cGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGCTGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTcgcg                                                                                                                                         >  2:84137/1‑150 (MQ=255)              aCAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGAc                                                                                                                                       >  2:567527/1‑150 (MQ=255)                  aaaaGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCt                                                                                                                                 <  2:130867/151‑1 (MQ=255)                       aTAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGc                                                                                                                            <  2:545428/151‑1 (MQ=255)                       aTAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGc                                                                                                                            >  2:67329/1‑151 (MQ=255)                            cGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGCCCACTACCAGTAGCGCCAACCCCCCAGCTTTTCGCGACA‑TTCTACCGCctc                                                                                                                         <  2:652395/149‑1 (MQ=255)                             ggAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCCCTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTg                                                                                                                       <  2:93761/150‑1 (MQ=255)                                aaaGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCACCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAAtt                                                                                                                   >  1:207852/1‑151 (MQ=255)                                 aaGCGACCAGCAAAAACCGCAAACCGGCCAGCATCAGCGGTGGCATTTTATGAACCCCCCCTTTGATGACCACAAAATTTACCCCCCATACGACCACTACCAGTATCGCCACCCCCCCATCTTTTCGCGACA‑TTCTCCCGCCTCTGAAttt                                                                                                                  <  2:275305/151‑1 (MQ=255)                                   gcgcCCAGCATAAAGCGCAACCCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCCCTTTGATGACCACAAAATTTAGCCCCCAAACGACCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTc                                                                                                                 <  1:273321/150‑1 (MQ=255)                                    cGACCAGCATAAAGCGCAAACGGCCCAGCATCAGCGGTGGCATTTTATGAAGCCCCACTTTAATGACCACAAAATTTAGCCCCCATACGCCCTCTCCCAGTAGCCCCAACACCCCATTTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCa                                                                                                                <  1:69621/150‑1 (MQ=255)                                    cGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCa                                                                                                                <  1:704347/150‑1 (MQ=255)                                      aCCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCt                                                                                                             >  2:771459/1‑151 (MQ=255)                                               aaGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGCCCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGc                                                                                                    <  1:562124/151‑1 (MQ=255)                                                     aacccGGCCAGCATCAGCGGGGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGCCCCCTCCCAGTAGCCCCAACCCCCCATCTTTCCGCGACA‑TCCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATc                                                                                                <  2:412523/146‑1 (MQ=255)                                                        ccGGCAAGCATCGGCGGTGGCATGTTATGAAGCCCCCCTTTGATGACCAAAAAATTTACCCCCCATCCGCCCACTACCATTAGCGCAAACCCCCCATCTTTTCCCGACT‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACtt                                                                                           <  2:204149/151‑1 (MQ=255)                                                          ggCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTCCCAGTAGCGCCACCCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAg                                                                                         <  1:748861/151‑1 (MQ=255)                                                            ccAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGCCCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCt                                                                                       <  1:73461/151‑1 (MQ=255)                                                            ccAGCATCAGCGGTGGCATGTTATGAACCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTCCCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCt                                                                                       <  1:603600/151‑1 (MQ=255)                                                              aGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCtt                                                                                                            >  2:585380/1‑128 (MQ=255)                                                              aGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGAGACCCACAAAATGTACCCCCCATACAACCCCTCCCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTCCCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTg                                                                                      <  2:612635/150‑1 (MQ=255)                                                                cATCAGCGGTGGCAGGTAAGGAAGCCCCATTTTGATAACCACAAAATTTAGCCCCCATACGCCCACTCCCAGTAGCGCCAACCCCCCATCTTTCCGCGACA‑TTCTACCGCCTCTGAATTTCATCtt                                                                                                            <  1:585447/126‑1 (MQ=255)                                                                     gCGGTGGCATGTTATGAACCCCCACTTTGATGACCAAAAAATTTAGCCCCAATCCGACCCCTACCATTAGCCCCACCACCCCATCTTTCCGCGCCA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACt                                                                              <  2:211706/151‑1 (MQ=255)                                                                          ggCATTTTATGAAGCCCCACTTTGATGCCCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCt                                                                         <  1:253730/151‑1 (MQ=255)                                                                           gCATGTTATGATGCCCCATTTTGATGCCCCCAAATTTTCGCCCCCATACGTCCACTCCCAGTAGCCCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCtt                                                                        <  1:176825/151‑1 (MQ=255)                                                                            ctttttgtaaatccccTCTTTGAGGACCACAAATGTGCGCCCCCACACGGCCACATCCAGGAGCGCAAACCCCCCTTCTTTAC‑CCACATTTTTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCtt                                                                        <  2:503817/138‑1 (MQ=255)                                                                                     aaGCCCCACTTTGATAACCACAAATTTTAGCCCCCATCCGACCATTACCAGTAGCCCAAACACCCCATCTTTTCGCGACA‑TTCTAACGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGa                                                              <  2:789099/151‑1 (MQ=255)                                                                                        ccccACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGAt                                                             <  1:740848/149‑1 (MQ=255)                                                                                           cACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTCCCAGTAGCGCCACCCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGtt                                                        <  1:171000/151‑1 (MQ=255)                                                                                              tttGATGACCACAAAATTTAGCCCCCATACGCCCACTACCAGTAGCGCCAACCCCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTa                                                       <  1:421251/149‑1 (MQ=255)                                                                                                 gatgaCCACAAAATTTAGCCCCAATACGACCACTGCCAGTAGCCCCAGCACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCg                                                   <  1:579428/150‑1 (MQ=255)                                                                                                   tgaCCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCg                                                >  2:454429/1‑151 (MQ=255)                                                                                                    gaCCACAAAATTTAGCCCCAATACTACCCCTACAATTAGCGCCACCCCCCCATTTTTCCGCGACA‑TATTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGcc                                                 <  2:487829/149‑1 (MQ=255)                                                                                                      ccACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGtt                                             >  2:22501/1‑151 (MQ=255)                                                                                                            aaTTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTacgacg                                       <  1:240523/151‑1 (MQ=255)                                                                                                             aTTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACgg                                      >  1:582467/1‑151 (MQ=255)                                                                                                                 aGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCAtt                                  >  2:340911/1‑151 (MQ=255)                                                                                                                           cgcccACTACCATTAGCGCAAACCCCCCATTTTTTCGCGACT‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATgcg                            <  2:490999/144‑1 (MQ=255)                                                                                                                               cACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATa                      >  2:780834/1‑149 (MQ=255)                                                                                                                                  tACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCg                 >  1:446180/1‑151 (MQ=255)                                                                                                                                        tAGCGCCACCCCCCCATCTTTTCGCGACT‑TTTTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCta              <  1:784775/148‑1 (MQ=255)                                                                                                                                         aGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACt          >  1:407158/1‑151 (MQ=255)                                                                                                                                           ccccAACACCCCATCTTTACGCGAAT‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCtata            <  1:107248/145‑1 (MQ=255)                                                                                                                                            gcCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCg       >  1:487089/1‑151 (MQ=255)                                                                                                                                                 cacCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGAttt  >  2:305473/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                       TTTCGGTCGTGCGACAAAAAAGATAGCCGGAAAAGCGACCAGCATAAAGCGCAAACCGGCCAGCATCAGCGGTGGCATGTTATGAAGCCCCACTTTGATGACCACAAAATTTAGCCCCCATACGACCACTACCAGTAGCGCCAACACCCCATCTTTTCGCGACA‑TTCTACCGCCTCTGAATTTCATCTTTTGTAAGCAATCAACTTAGCTGAATTTACTTTTCTTTAACAGTTGATTCGTTAGTCGCCGGTTACGACGGCATTAATGCGCAAATAAGTCGCTATACTTCGGATTT  >  NC_000913/1620973‑1621267

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑