Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,140	0	A	G	21.4%	143.6 / 11.2	70	intergenic (+123/‑75)	lldD/trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base A (39/16);  new base G (1/14);  total (40/30)
Fisher's exact test for biased strand distribution p-value = 8.28e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGA  >  NC_000913/3781041‑3781237                                                                                                      |                                                                                                  cccTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGgaga                                                                                                   >  2:1192739/1‑100 (MQ=255) cccTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGgaga                                                                                                   <  2:2200298/100‑1 (MQ=255)  ccTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGagag                                                                                                  >  1:2037830/1‑100 (MQ=255)  ccTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACAACGCACGCTTTTTTTGTCCCTCGCCCCTCC‑GGGGagag                                                                                                  >  2:1550978/1‑100 (MQ=255)    tctcCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAggg                                                                                                <  1:2094048/100‑1 (MQ=255)       cccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCg                                                                                             >  1:1228435/1‑100 (MQ=255)       cccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCg                                                                                             >  1:1597351/1‑100 (MQ=255)        ccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCgg                                                                                            <  1:2079685/100‑1 (MQ=255)         ttccgatctagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCgg                                                                                            <  1:2289164/90‑1 (MQ=255)         cgccgggAGAGGGGACCGTTCGGCGCTGTATGTACTTCCTCGCTCTCAAA‑CGACACCGTACTCTTTTTTTCTCACCCGCCCCTCC‑AGGGCGGGGGCCg                                                                                             >  2:2055795/5‑98 (MQ=255)           cAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGt                                                                                         >  2:846011/1‑100 (MQ=255)               gagaGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAgg                                                                                     >  1:1822341/1‑100 (MQ=255)                agagGGGACCGTTCGGCGCTGTATGTCCTCCCTCCATCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCTGTGTGAggg                                                                                    <  2:997874/100‑1 (MQ=255)                 gagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAgggg                                                                                   <  1:729121/100‑1 (MQ=255)                  agGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCggagatcggaag                                                                                  >  2:2289153/1‑90 (MQ=255)                  agGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGa                                                                                  <  2:316937/100‑1 (MQ=255)                   ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGaa                                                                                 >  2:361074/1‑100 (MQ=255)                   ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGaa                                                                                 <  1:639763/100‑1 (MQ=255)                      gACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAg                                                                              <  1:951369/100‑1 (MQ=255)                          gTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCg                                                                          >  1:1253551/1‑100 (MQ=255)                          gTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCg                                                                          >  1:2305000/1‑100 (MQ=255)                             cGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCAc                                                                       >  2:2200545/1‑100 (MQ=255)                              ggCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACt                                                                      >  1:1287536/1‑100 (MQ=255)                              ggCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACt                                                                      >  2:809420/1‑100 (MQ=255)                                cgcTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGc                                                                    >  2:1358168/1‑100 (MQ=255)                                cgcTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGc                                                                    >  1:102883/1‑100 (MQ=255)                                cgcTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGc                                                                    >  1:150450/1‑100 (MQ=255)                                       tgtaCTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCAcc                                                               >  2:1028710/1‑98 (MQ=255)                                         tccTCCCTCACCCTGAAA‑CGACCCCGCACTTTTTTTTCCCCCCCCCCCCCCCG‑GGGGAGAGGCCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAAtt                                                           <  2:1287533/98‑1 (MQ=255)                                         taCTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTTTTTTTTTCCCCTCC‑GGGGAGAGGGCCGGGGTGTGGGGAAAAGGCCGCACTGCTCACCAAtt                                                           >  2:1853853/1‑100 (MQ=255)                                         taCTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAAtt                                                           >  2:2208557/1‑100 (MQ=255)                                         taCTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAAtt                                                           >  2:720988/1‑100 (MQ=255)                                            tCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTc                                                        >  2:1209022/1‑100 (MQ=255)                                             ccccccctatGAAA‑CGCCACCGCTCTCTTTTTTTCTCCCCCGCCCCCCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                       <  2:102884/91‑1 (MQ=38)                                             ccccCACTCGGAAA‑CAACACCGCCCTCTTTTTTTCCCCCCCCCCCCCCC‑GGGAAGAGGGCGGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                       <  2:1500781/100‑1 (MQ=255)                                             cccTCACTCTGAAA‑CGACACCGCCCTTTTTTTTTCTCCCTCCCCCCTCG‑GGGGGGAGGGCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                       <  1:2143907/100‑1 (MQ=255)                                             cccTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCTCTCCTCC‑GGGGAAAGGGCCGGGGTGAGGGGAAAAGGCGGCACTGCtgaactat                                                            >  2:2192288/1‑88 (MQ=38)                                             cccTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                       >  1:1051583/1‑100 (MQ=255)                                             cccTCA‑TCTGAAATCGCCCCCGCCTTCTTTCTTCCCCCCCCGCCCCTCG‑GGGAAGGGGGCGGGGGGGGGGGAAAAAGGCCGCACTGCTCACCAATTTTc                                                        <  1:190427/99‑1 (MQ=255)                                              ccTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg                                                      >  1:472378/1‑100 (MQ=255)                                              ccTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg                                                      >  2:153652/1‑100 (MQ=255)                                               ctctcttgcaaa‑CGACACGCCCCTTTTTTTTTCCCCCCCGCCCCCCG‑GGGGGGGGGGCGGGGGTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                     <  2:1735292/91‑1 (MQ=255)                                               ctctctctGAAA‑CGACCCCCCCCTTTTTTTTTCCCCCTCCCCCCCCG‑GGGGAGGGGGCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                     <  1:2259143/100‑1 (MQ=255)                                               cgccctctGAAC‑CGCCGCGGCACGTTTTTTTGCCCCCGCCCCCCGCC‑GGGGAGGGGCCCGGGGTGAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                     <  2:1390468/96‑1 (MQ=255)                                               cTCCCTCTGAAA‑CGACCCCGCCCTCTTTTTTCCCCCCTCCCCCCCCG‑GGGGGGGGGGCCGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                     <  2:1228432/100‑1 (MQ=255)                                                   ctctGAAA‑CGACACCGCACTCTTTTTTTTTTTTTTTTTCATCC‑GGGGAGAGGGCCGGGGTGTGTGTAAAAGGCCGCACTGCTCACCAATTTTCTGCTAt                                                  >  2:1116145/1‑99 (MQ=255)                                                      tGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTg                                              >  2:1543140/1‑100 (MQ=255)                                                       gAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc                                             >  2:980257/1‑100 (MQ=255)                                                       gAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc                                             >  2:310635/1‑100 (MQ=255)                                                        aaa‑CGCCGCCGCGCTCTTTTTTTCTCCCGCCCCCCGCC‑GGGGAGAGGGCCGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCt                                                    <  2:150451/92‑1 (MQ=255)                                                              acacCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGc                                       >  1:330962/1‑100 (MQ=255)                                                               cccccccctctTTTTTCCCCCCCCCCCCCTCC‑GGGGGGGGGGCGGGGGGGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCa                                      <  1:1281532/93‑1 (MQ=255)                                                                 ccGCACTCTTTTTTTTTTTTTCTCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACt                                    >  2:1827792/1‑100 (MQ=255)                                                                  ccccccttttttttCCCCCCCCCCCCCCCGGGGGGGGGGGCGGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                     <  1:799720/92‑1 (MQ=255)                                                                  cGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCaaga                                   >  1:323663/1‑97 (MQ=255)                                                                   gcgctttttttttCTCCCTCGCCCCCCG‑GGGGGGGGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTa                                   <  2:472380/93‑1 (MQ=255)                                                                    cccttttttttcCCCCCCCCCCCCCCC‑GGGGAGGGGGCCGGGGGGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAg                                 <  1:361072/95‑1 (MQ=255)                                                                     ccttttttttcCCCCCCCCCCCCCCC‑GGGGGGGGGGCGGGGGTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                     <  2:681689/91‑1 (MQ=255)                                                                      ctctTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCGCTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggg                               >  1:1653982/1‑100 (MQ=255)                                                                        ctTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                             >  1:929382/1‑100 (MQ=255)                                                                        ctTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                             >  1:1720343/1‑100 (MQ=255)                                                                         tttttttCTCCCTCCCCCCCCG‑GGGGGGGGGGCGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCa                                      <  2:323665/90‑1 (MQ=255)                                                                         ttttttcCCCCCTCCCCCCCCG‑GGGGAGGGGCCCGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGc                            <  1:1209025/100‑1 (MQ=255)                                                                            ttttCCCCCTCGCCCCGCG‑GGGGGGGGGGCCGGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAg                          <  2:1881166/99‑1 (MQ=255)                                                                                 tcCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCt                    >  1:730633/1‑100 (MQ=255)                                                                                  cccTCGCCCCCCC‑GGGGGGAGGGCCGGGGTGTGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTa                   <  2:1253548/100‑1 (MQ=255)                                                                                    cTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa                 >  1:368878/1‑100 (MQ=255)                                                                                    cTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa                 >  2:1594094/1‑100 (MQ=255)                                                                                     cccccccccC‑GGGGAGGGGGCCGGGGGGAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAAc                <  1:846013/97‑1 (MQ=255)                                                                                           cccc‑ggggggggggccggggggggggAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt           <  2:55202/97‑1 (MQ=255)                                                                                           cTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTa          >  1:616786/1‑100 (MQ=255)                                                                                            tCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTAc         >  2:1153517/1‑100 (MQ=255)                                                                                              c‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACtt       >  1:1117479/1‑100 (MQ=255)                                                                                                ggggAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACttt      <  2:368880/100‑1 (MQ=255)                                                                                                 gggAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTa     <  1:1153520/100‑1 (MQ=255)                                                                                                    agagGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGa  >  2:244331/1‑100 (MQ=255)                                                                                                      |                                                                                                  CCCTCTCCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAA‑CGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCC‑GGGGAGAGGGCCGGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGA  >  NC_000913/3781041‑3781237

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑