Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	345,328	0	C	A	56.1%	45.0 / 94.7	57	intergenic (+337/‑76)	yahL/yahM	uncharacterized protein/uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base C (22/3);  new base A (0/32);  total (22/35)
Fisher's exact test for biased strand distribution p-value = 6.59e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.81e-11

ATGATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCAAAGTGGAAC  >  NC_000913/345184‑345471                                                                                                                                                 |                                                                                                                                                aTGATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCaaaaa                                                                                                                                            >  2:142286/1‑150 (MQ=255) aTGATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAAc                                                                                                                                           <  1:455816/151‑1 (MQ=255)   gATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCg                                                                                                                                         >  2:475491/1‑151 (MQ=255)    aTCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCg                                                                                                                                         >  1:671224/1‑150 (MQ=255)        cATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCAtt                                                                                                                                    >  1:664931/1‑151 (MQ=255)              gATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCtca                                                                                                                              >  1:302890/1‑151 (MQ=255)                    ttGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGa                                                                                                                        >  2:337621/1‑151 (MQ=255)                       tgAATGTTTTGTTTGACATTAATATAAAAAAAATCATAATCCCACCATGTTTGTGTGGGTTTTTTTCTTTATCTTACGCACCGCCCCCAACCTTGAAAAAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAag                                                                                                                      <  1:108094/150‑1 (MQ=255)                            gtgtTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAga                                                                                                                >  2:782572/1‑151 (MQ=255)                                      aCATTCATATGAAAAAAATCATATTCCCATCATGTTGGTGTGGGTTTTTTTTTTTTTCTTCCGCACCCCCCTAAACCCTGACAAAAAATAGGCTGAAAGCCTAAAAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCa                                                                                                       <  1:765831/150‑1 (MQ=255)                                      aCATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAg                                                                                                      >  1:375647/1‑151 (MQ=255)                                          aaatagaaaaaaaaTCAAACTTCACCAATTTTTGTGTGGGTTCTTTTCTGTATTTTACAAATCTCTCTGACCCGTGATAAAAAATTTATTGTAAGTCCCATAAAAAAAGCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAtt                                                                                                  <  1:746643/144‑1 (MQ=255)                                           aaaatGAAAAAAATCAAATTTAAAAACTGTTTGTGGGGGGTTTTTTCTGTTTCTTACGTAGCGCACGCAGGCCTGAAAGAAAATATGTTGTAGGCCTCAAAGAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttg                                                                                                 <  2:28064/148‑1 (MQ=255)                                              ataaaaaaaaTAATAATCCCATCATGTTTGTGTGGGTTTTTTTCTGTATCTTCCGCATCGCCCTCAAGCCTAACAAAAAATAGGCTGTAAGGCTAATATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgttg                                                                                              <  1:95748/148‑1 (MQ=255)                                              aaaaaaaaaaCAATAATCCCATCGTTTTTGTGTGGGGTTTTTTCTGTATCTTCCGCAGCGCACGAAAGCCTGACAAAAAATATGCTGTATGTCTAATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGAttgttg                                                                                              <  2:251568/148‑1 (MQ=255)                                                 aaaaaaaTAATAATTCCATAATTTTGGGGGGGGGTTTTTTCTTTATTTAACGCATCCCACCAAAGCCTGAAAAAAAATAGGCTGTAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAt                                                                                           <  2:728968/151‑1 (MQ=255)                                                 aaaaaaaTAATAATCCCATATTGTTGGGGGGGGGTCTTTTTTTTATCTTCCCCCCCGCACCCAAGCCGGAAAAAAAATATGCTGAAAGGCTAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTAt                                                                                           <  2:117909/151‑1 (MQ=255)                                                   aaaaaTCATAATCCCATCATGTTTGTGGGGGGTTTTTTCTGTATCTTACGCCTCGCACTCAAGCCTGAAAAAAAATATGCTGTAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATgg                                                                                         <  2:114772/151‑1 (MQ=255)                                                   aaaaaTCATAATCCCATAATGTTTGGGGGGGTTTTTTTCTGTTTCTTCCGCACCCCACTAAAGCCTGAAAAAAAATATGCTGTAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATgg                                                                                         <  2:42331/151‑1 (MQ=255)                                                   aaaaaTAATAATCCCTTCATGTTTGGGTGGGGTTTTTTCTTTATCTTCCGCCCCGCCCTCAAGCCTAACAAAAAATATGCTGAAAGGCACATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATgg                                                                                         <  1:281461/151‑1 (MQ=255)                                                     aaaTCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTa                                                                                       >  1:628996/1‑151 (MQ=255)                                                      aaTCATAATCCCATCATGTTTGTGGGGGGTTTTTTCTGTATCTTCCCCACCCCACTAAAGCCTGAAAGAAAATAGGCTGTAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTAc                                                                                      <  2:116391/151‑1 (MQ=255)                                                          aTAATCCCATCTTTTTTGTGGGGGGTTTTTTCTGTATCTTCCGCACCGCACTCAAGCCTGAAAAAAAATTTGCTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACgggg                                                                                  <  2:235151/151‑1 (MQ=255)                                                                ccATCATTTTTGTGGGGGGTTTTTTCTGTATCTTCCGCACCGCCCTCAAGCCTGAAAAAAAATATGCTGTAAGGCTAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAg                                                                            <  2:450359/151‑1 (MQ=255)                                                                  ataatGTTTGTGTGGGGTTTTTTCTTTAGCTTACGCACCGCACTCAACCCTAAAAAAAAATATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGc                                                                          <  1:411798/148‑1 (MQ=255)                                                                     atGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCt                                                                        >  2:600489/1‑150 (MQ=255)                                                                     atGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCt                                                                        >  1:618903/1‑150 (MQ=255)                                                                       gTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGa                                                                     >  1:694090/1‑151 (MQ=255)                                                                          tgtgtgGGTTTTTTTCTTTATCTTACCCCTCGCTCACAACCCAGACAAAAAATGTGGTGAAGGGCTTATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATgg                                                                  <  1:585961/151‑1 (MQ=255)                                                                                     ttttctttttctTCCCCACCCCACTCAACCCTAAAAAAAAATATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACtt                                                       <  2:66342/151‑1 (MQ=255)                                                                                      tttCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACttt                                                      >  2:742589/1‑151 (MQ=255)                                                                                      tttCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACttt                                                      >  2:150022/1‑151 (MQ=255)                                                                                             ttcttacctaccccACCCAACCCAGACAGAAAATGAGTTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAAc                                               <  1:565314/138‑1 (MQ=255)                                                                                             aTCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCaaaa                                                >  2:63259/1‑150 (MQ=255)                                                                                               cTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAAct                                              >  2:594424/1‑150 (MQ=255)                                                                                                          cACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAg                                  >  1:686458/1‑151 (MQ=255)                                                                                                            ccaaagccgaaaaaaaaaTATTGTGTAGGCCTCATACAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGGCAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGAt                                <  2:365990/137‑1 (MQ=255)                                                                                                            cTCAACCCTGAAAAAAAATATGCTGTAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGAt                                <  2:551477/151‑1 (MQ=255)                                                                                                               aaGCCAAACAAAAAATATGGTGAAAGGCAAATAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATccc                             <  1:309266/151‑1 (MQ=255)                                                                                                                accctaaaaaaaaaTATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATcccc                            <  2:450548/141‑1 (MQ=255)                                                                                                                 gCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATccc                             >  2:795773/1‑149 (MQ=255)                                                                                                                      aaaaaaaaTATGCTTAAAGGCTCATATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCttatta                      <  2:569931/147‑1 (MQ=255)                                                                                                                      aaaaaaaaTAGGCTGTAAGGCTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCttatta                      <  2:318882/147‑1 (MQ=255)                                                                                                                      aaaaaaaaGATGCTGAAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCttatta                      <  2:750008/147‑1 (MQ=255)                                                                                                                      aCAAAAAATATGTTAAAGGGTTCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCttatta                      <  2:658948/151‑1 (MQ=255)                                                                                                                      aCAAAAAATATGCTAAAAACCTCTTAAAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCTAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCttatta                      <  2:739171/151‑1 (MQ=255)                                                                                                                        aaaaaaTATCCTGTACGGCTAAATTAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTGCAAAACTCTTCTGAATCAGATCCCCTtattat                     <  2:95293/148‑1 (MQ=255)                                                                                                                         aaaaaTATGCTATAAGGCTAATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatca                   <  2:235609/150‑1 (MQ=255)                                                                                                                          aaaaTATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatcat                  >  1:134189/1‑151 (MQ=255)                                                                                                                           aaagagacTGTAAGGCTAAAATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatcatc                 <  1:510648/144‑1 (MQ=255)                                                                                                                           aaaTGTGTTGTAAGCACCATATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatcatc                 <  1:216199/151‑1 (MQ=255)                                                                                                                           aaaTATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatcat                  >  2:169836/1‑150 (MQ=255)                                                                                                                           aaaTATGCTGAAAGGCTAATATAAAAACCCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatcatc                 <  1:397108/151‑1 (MQ=255)                                                                                                                           aaaTATGCTGAAAGCCTCAAATAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTatcatc                 <  1:167733/151‑1 (MQ=255)                                                                                                                               atGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATcc                >  2:57024/1‑148 (MQ=255)                                                                                                                                  cTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCaa          >  1:603299/1‑151 (MQ=255)                                                                                                                                          ataatatAAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCAAAGTGGAAc  <  1:458793/148‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                ATGATCTCATGCAGATGTTTTGTGAATGTGTTGGTTGACATTCATATGAAAAAAATCATAATTCCATCATGTTTGTGTGGGGTCTTTTCTGTATCTTACGCATCGCACTCAAGCCTGACAGAAAATATGCTGTAAGGCTCATATCAAAAACCGCCATTAGCTCATCAGGAAGAGCAGACGACAACCAGGATTGTTGTATGGTACGGGGTTCGAGGCCTCGATGGCGGTCCAACTTTTCAAAACTCTTCTGAATCAGATCCCCTTATTATCATCCCTGCAAAGTGGAAC  >  NC_000913/345184‑345471

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑