Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,443,277	0	A	C	40.4%	114.2 / 13.3	57	V274G (GTA→GGA)	secY	preprotein translocase membrane subunit
Reads supporting (aligned to +/- strand):  ref base A (32/2);  new base C (0/23);  total (32/25)
Fisher's exact test for biased strand distribution p-value = 5.65e-14
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTA  >  NC_000913/3443132‑3443421                                                                                                                                                    |                                                                                                                                                 cGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑Accccc                                                                                                                                             <  1:988973/151‑1 (MQ=255)    aTAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGcc                                                                                                                                          >  2:276177/1‑151 (MQ=255)     tAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGcc                                                                                                                                          >  2:1111614/1‑150 (MQ=255)        agTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCatat                                                                                                                                      >  1:187008/1‑151 (MQ=255)         gTAACAAATAAGGCGGTTGCCGAGGCTCCAAATACAGCAAAATTGTTGTCAGCCAGTTCAAACCG‑GTCCCGCCCCCGAACCATGACGCGATGGGCGCCGGGAACAGAAAAATCTTGGAGGCGAGGATTGCCGGGATT‑ACCCCCGCCatat                                                                                                                                      <  2:744872/150‑1 (MQ=255)             cacaTAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACt                                                                                                                                 >  2:287317/1‑151 (MQ=255)              acaTAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGCTT‑ACCCCCGCCATATTCACtt                                                                                                                                >  1:608497/1‑151 (MQ=255)              acaTAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGACTGCCGGGATT‑ACCCCCGCCATATTCACtt                                                                                                                                >  1:950324/1‑151 (MQ=255)                aTAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTc                                                                                                                              >  1:175247/1‑151 (MQ=255)                 tAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTc                                                                                                                              >  1:1062225/1‑150 (MQ=255)                       ggTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGt                                                                                                                        >  1:687483/1‑150 (MQ=255)                           gCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAAtg                                                                                                                   >  2:976363/1‑151 (MQ=255)                               agcctcaaaaCACAGCAAATTTTTTGTCCCCCA‑TTCCAACCAGGTCCCCCCCCCGACCCATGCCGCGAGGGTGGCGGGAAAAAAAAAAATCGTGAAAGCGAAGTTGGCGGGAATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAAtgtgtg                                                                                                               <  2:364173/144‑1 (MQ=255)                                    gCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCtg                                                                                                          >  1:531087/1‑151 (MQ=255)                                     cAACTACAGCGAAATTGGTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCTCCGGGAACTGAATAATACTGGAAGCGAAGATTCCTGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGGAAATGTGTGCTCtgt                                                                                                         >  2:104507/1‑151 (MQ=255)                                     cAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCtgt                                                                                                         >  2:975869/1‑151 (MQ=255)                                      aaaTACAGCGAATTTTTTTCCCCCCAGTCCCCACCA‑GCCCCCCCCCAGAACCAGGACGGGGTGGTCGCCGGAAAAAAAATAATATGGGAAGGAAAGA‑TGGCGGGATTCCCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGctct                                                                                                           <  2:85556/148‑1 (MQ=255)                                      aaaTACAGCAAATTTGTGGTCAGCATGTCCCACCCA‑GCCCCCCCCCCGACCAAGGGCGCGTTGGCCGCGGGGAAAAAAATAATCGGGAAAGCAAAGTTTGCGGGGATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCtgt                                                                                                         <  1:960454/150‑1 (MQ=255)                                       aaTACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTgc                                                                                                       >  2:226545/1‑151 (MQ=255)                                             gCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCAt                                                                                                  >  2:1019597/1‑150 (MQ=255)                                                   ttgttgTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACacg                                                                                           >  2:938769/1‑151 (MQ=255)                                                     gttgtCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACacgac                                                                                         >  2:309617/1‑151 (MQ=255)                                                      ttgtCAGCAATTCCCAACCA‑GTCCCGCCCCCGAACCATGACGCGATGGGCGCGGGAAAAAAAAAAATACTGGAGGCGAAGATTGCGGGGATC‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACacgac                                                                                         <  1:249397/150‑1 (MQ=255)                                                        gtCAGCCAGTTCCAACCA‑GTACCG‑CCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGAcc                                                                                     >  2:300853/1‑151 (MQ=255)                                                            gCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTg                                                                                  >  2:449859/1‑151 (MQ=255)                                                               aGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTg                                                                               >  1:1006776/1‑151 (MQ=255)                                                                   ccAACCA‑GTCCCGCCCCCGAACCAGGACGGGATGGTCGCGGGAAAAAAAATAAGACTGGAGGCAAAGATTGCCGGTTTT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGAc                                                                             <  2:264786/149‑1 (MQ=255)                                                                    cAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGtt                                                                          >  1:742110/1‑151 (MQ=255)                                                                     aaCCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGttt                                                                         >  1:855557/1‑151 (MQ=255)                                                                     aaCCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGttt                                                                         >  2:727442/1‑151 (MQ=255)                                                                        ccagccccccccccGAACAATGGCGGGATGGTCGCCGGAAAAAAAATAATACTGGAAGCAAAATTTGCCGGTATC‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGc                                                                                 <  2:308894/132‑1 (MQ=255)                                                                         cagccccccccccGAACCATGACGGGATGGTCGCCGGGAAAAAAATAATACTGGAAGCGAAGATTGCCGGGATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGtt                                                                          <  1:902766/139‑1 (MQ=255)                                                                              cccccccacacccAGGACGCGATGGTCGCCGGAAACAAAATAATACGGGAAGGGAATATTGCCGGGTTT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGt                                                                 <  1:886/140‑1 (MQ=255)                                                                                    ccGACCCATGACGCGGTGGTCGCGGGAAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACca                                                           <  1:599748/151‑1 (MQ=255)                                                                                    ccGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTAcc                                                            >  1:490661/1‑150 (MQ=255)                                                                                         ccATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATg                                                      >  2:886106/1‑151 (MQ=255)                                                                                                gcgGTGGTTGCCGGGAACAAAAAATTACTGGAAGGGAAGATGGCGGAGCTT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATgcggc                                                  <  1:440094/148‑1 (MQ=255)                                                                                                  ggtGGGCGCCGGAAAAAAAATAAATGTGGAAGCGAAGATCGCCAGAATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTg                                              <  2:580801/148‑1 (MQ=255)                                                                                                  gATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTg                                              >  2:200703/1‑150 (MQ=255)                                                                                                        cGCCGGGAACAGAAAAAAAGTGGAAGCGAAGTTTGCGGGGATC‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGc                                       <  2:354374/151‑1 (MQ=255)                                                                                                               aaaaaaataatACTGGAAGCAAAGTTTGCGGGGATC‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaacaa                                <  2:905796/146‑1 (MQ=255)                                                                                                                aaaaaataatACGGGAAGCGAAGATTGCGGGGATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACaaa                               <  1:121055/147‑1 (MQ=255)                                                                                                                aCAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTcaacaa                                >  1:1006349/1‑150 (MQ=255)                                                                                                                 cAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAAt                              >  1:402878/1‑151 (MQ=255)                                                                                                                    aataatACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATac                            >  1:889986/1‑150 (MQ=255)                                                                                                                       attattGGAAGGGAAGATTGCGGGAATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATacaa                          <  2:146671/144‑1 (MQ=255)                                                                                                                       aatccgggAAGCGAAGCCTGCCGGGATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATacaaca                        <  2:950179/145‑1 (MQ=255)                                                                                                                        ataCTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATacaaca                        >  2:118235/1‑150 (MQ=255)                                                                                                                          acgggaagggaagATGGCGGGGATC‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACaaa                      <  2:186968/147‑1 (MQ=255)                                                                                                                                agagAAGATTGCCGGGATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAAc                  <  1:606333/145‑1 (MQ=255)                                                                                                                                  cGAATATTGCGGGGATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGt                <  2:905555/148‑1 (MQ=255)                                                                                                                                  cGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCAc             >  1:198211/1‑151 (MQ=255)                                                                                                                                   gAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACt            >  2:1037998/1‑151 (MQ=255)                                                                                                                                    aaGATTGCCGGAATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCa              <  1:521365/148‑1 (MQ=255)                                                                                                                                        tgccggggATC‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGt                <  2:687363/137‑1 (MQ=255)                                                                                                                                             gggTTT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatacta  <  1:287373/151‑1 (MQ=255)                                                                                                                                             gggATT‑CCCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAaatact   <  2:512483/150‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                 CGCATAGAGTAACACATAAAGCGGTTGCCCAGGCTGCAAATACAGCGAAATTGTTGTCAGCCAGTTCCAACCA‑GTACCGCCCCCGAACCATGACGCGATGGTCGCCGGGAACAGAATAATACTGGAAGCGAAGATTGCCGGGATT‑ACCCCCGCCATATTCACTTTCAGCGGTAAATGTGTGCTCTGTGCAGCATAGACACGACGACCTTGCTGACGTTTCGCGTAGTTTACCACAATGCGGCGTTGACCACGCTCAACAAATACAACAAAGAACGTCACTGCAAATACTA  >  NC_000913/3443132‑3443421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑