Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,140	0	A	G	24.7%	145.6 / 10.9	73	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 (42/13);  new base G (0/18);  total (42/31)
Fisher's exact test for biased strand distribution p-value = 3.75e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAC  >  NC_000913/3781047‑3781235                                                                                               |                                                                                                  cccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑g                                                                                            >  2:61092/1‑100 (MQ=255) cccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑g                                                                                            >  2:1144851/1‑100 (MQ=255) cccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑g                                                                                            >  2:1328528/1‑100 (MQ=255) cccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑g                                                                                            >  2:360399/1‑100 (MQ=255) cccTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGAAACCGCACTCTTTTTTTCTCCATC‑GAACATCCGGGGaaag                                                                                                  >  2:964745/1‑95 (MQ=255)   cTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑ggg                                                                                          <  1:1842885/100‑1 (MQ=255)    tCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTTTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑gggg                                                                                         <  1:1420341/100‑1 (MQ=255)    tCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑gggg                                                                                         <  1:2167194/100‑1 (MQ=255)     gaGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGt                                                                                        >  1:1249280/2‑100 (MQ=255)     cAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGt                                                                                        <  1:1766572/100‑1 (MQ=255)        ggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAg                                                                                     <  2:162704/100‑1 (MQ=255)        ggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAg                                                                                     >  2:1316153/1‑100 (MQ=255)         gagaGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAgg                                                                                    >  2:246843/1‑100 (MQ=255)          agagGGGACCGTTCGGCGCTGTATGTTCTCCCTCTCTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAggg                                                                                   <  2:25587/100‑1 (MQ=255)          agagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAggg                                                                                   <  2:308573/100‑1 (MQ=255)          agagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAggg                                                                                   <  2:1533686/100‑1 (MQ=255)             ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑aa                                                                               >  1:507244/1‑100 (MQ=255)             ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑aa                                                                               >  2:2049031/1‑100 (MQ=255)             ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑aa                                                                               >  2:1805788/1‑100 (MQ=255)             ggggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑aa                                                                               >  2:366106/1‑100 (MQ=255)              gggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑aaa                                                                              >  1:1520488/1‑100 (MQ=255)              gggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑aaa                                                                              <  1:70411/100‑1 (MQ=255)              gggACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTGTCTCCCTC‑GCCCCTCCGTGGAGAGGGCC‑GCGGTGAGGGG‑aaa                                                                              >  1:1559618/1‑100 (MQ=255)                gACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAg                                                                            >  2:2161793/1‑100 (MQ=255)                         gcgcTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTTTCCCTC‑TCTCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTg                                                                   >  1:1179346/1‑100 (MQ=255)                             tgtatgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGGGAGGGG‑AAAAGGCCGCCCTGCTCa                                                               >  2:38134/1‑100 (MQ=255)                               tatgtcCCCCCTCCCTCTGAAACGACCCCGCCCT‑TTTTTTTCCCCCCC‑CCCCCCCCGGGGGGGGGGCC‑GGGGGGGGGGGAAAAAGGCCGCACTGCTCAc                                                              <  1:2161781/99‑1 (MQ=255)                                 tgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCaa                                                           >  2:1077047/1‑100 (MQ=255)                                 tgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCaa                                                           >  2:1350998/1‑100 (MQ=255)                                   taCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAAtt                                                         >  2:1384773/1‑100 (MQ=255)                                     cTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAAtttt                                                       >  2:600680/1‑100 (MQ=255)                                       ccccccctctGAAACGACCCCGCCCTCTTTTTTCCCCCCCC‑CCCCCTCGGGGGAGGGGGCG‑GGGGGGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCt                                                     <  2:1389266/94‑1 (MQ=255)                                       cccTCACTCTGAAACGACACCGCGCTTTTTTTTTCCCCCTC‑GCCCCCCCGGGGGGGGGGCC‑GGGGTGGGGGA‑AAAAGGCCGCACTGCTCACCAATTTTCt                                                     <  1:168898/100‑1 (MQ=255)                                       cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCt                                                     >  1:396201/1‑100 (MQ=255)                                       cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCt                                                     >  1:1482791/1‑100 (MQ=255)                                       cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCt                                                     >  1:323802/1‑100 (MQ=255)                                       cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCt                                                     >  1:320727/1‑100 (MQ=255)                                         cccACTCTGAAACGACACCGCACTCTCTTCTTCTCCCTC‑GCCCCTCCGGGGATAGGGCC‑GGGGTGAGGGG‑CAAAGGCCGCACTGCTGACCAATTTTCTGc                                                   >  1:527397/3‑100 (MQ=38)                                         cTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGc                                                   >  1:9527/1‑100 (MQ=255)                                           ccctcgGAACCGCCCCCGCCCTCTTTTTTCCCCCCCC‑GCCCC‑CCGGGGGGGGGGCCGGGGGGGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGc                                                   <  1:181313/96‑1 (MQ=255)                                              gttGAACCTACACCGCCCTCTTTTTCTCCCCCTC‑CCCTACCGGGGGGGAGGGCA‑GGGGTGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATcc                                              <  2:1534937/98‑1 (MQ=255)                                               ctacaaCGGCCCCGCCCTCTTTTTTTCTCCCTC‑GCCCCCCCGGGGAGAGGGCC‑GGGTTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATcc                                              <  1:264759/95‑1 (MQ=255)                                               ctGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCt                                             >  1:1948949/1‑100 (MQ=255)                                               cggAAACGACACCGCACTCTTTTTTTCTCCCGC‑GCCCCCCGGGGGAGGGGGCC‑GGGGTGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGc                                                   <  1:2133748/92‑1 (MQ=255)                                                 gAAACGACACCGCACTCTTTTTTTCTTTTTT‑GTCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc                                           >  1:1971310/1‑100 (MQ=255)                                                   aaactcacCGCCCTTTTTTTTTCCCCCCC‑CCCCCCCCGGGGAAGGGGCCGGGGGGGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTa                                                 <  2:260328/88‑1 (MQ=255)                                                   aaCGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGccc                                         >  1:386971/1‑100 (MQ=255)                                                         acgaccccctTTTTTTGTCCCCC‑CCCCCACGGGGGAAGGGGCG‑GGGGTGTGGGT‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                   <  2:1925484/92‑1 (MQ=255)                                                          ccgtattttttttttCTCCCTC‑GCCCCGCGGGGGGGGGGGCG‑GGGGGGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCa                                    <  1:946023/90‑1 (MQ=255)                                                          ccGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                   >  1:675204/1‑99 (MQ=255)                                                          ccGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACt                                  >  2:1434647/1‑100 (MQ=255)                                                            gccctctTTTTTTCTCCCTC‑CCCCCGCGGGGGGGGGGGCC‑GGGGGGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCAc                                   <  1:1229513/94‑1 (MQ=255)                                                                tttttttttCCCCCCC‑GCCCCCCGGGGGGGAGGGCG‑GGGGTGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAgggg                            <  1:31402/98‑1 (MQ=255)                                                                 ctTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                           >  1:73653/1‑100 (MQ=255)                                                                 ctTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                           >  1:1880742/1‑100 (MQ=255)                                                                  ttttttcCCCCCTC‑CCCCCCCGGGGGGGGGGGCC‑GGGTGGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGc                          <  2:1520495/100‑1 (MQ=255)                                                                  ttttttcCCCCCCC‑CCCCCCCGGGGGGGGGGGCC‑GGGGTGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                           <  1:61092/99‑1 (MQ=255)                                                                   ttttttCCCCCCC‑CCCCCCCCGGGGGGGGGGCCGGGGGTGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGc                          <  2:1249282/100‑1 (MQ=255)                                                                    tttttCCCCCCC‑GCCCCCTGGGGGAGGGGGCC‑GGCGCCAGCAG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAg                        <  2:564936/100‑1 (MQ=255)                                                                     ttttCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGt                       >  2:391877/1‑100 (MQ=255)                                                                     ttttCCCCCCCGGCCGCTCGGGGGGGGGGCCC‑GGGGGGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAg                        <  1:1328526/100‑1 (MQ=255)                                                                            ccccccccccccGGGGGGGGGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCt                  <  1:1536847/93‑1 (MQ=255)                                                                            ccTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAACGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaa                >  1:821814/1‑100 (MQ=255)                                                                             cTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa               >  2:2101630/1‑100 (MQ=255)                                                                             cTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa               >  1:343733/1‑100 (MQ=255)                                                                                  ccccTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATc           >  1:1578585/1‑100 (MQ=255)                                                                                  ccccGCGGGGGGGGGGGCG‑GGGGTGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTa                 <  1:2068995/94‑1 (MQ=255)                                                                                    ccTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTTCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt         >  2:614281/1‑100 (MQ=255)                                                                                    ccTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt         >  2:1685489/1‑100 (MQ=255)                                                                                       cgggggAGGGGGCG‑GGGGGGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTAc       <  1:2084499/97‑1 (MQ=255)                                                                                         ggggAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACttt    >  1:1539633/1‑100 (MQ=255)                                                                                          ggggGAGGGCC‑GGGGTGGGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTa   <  1:391876/100‑1 (MQ=255)                                                                                           ggAGGGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAc  <  1:1701281/100‑1 (MQ=255)                                                                                           ggAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAc  >  1:1976929/1‑100 (MQ=255)                                                                                              gagGTCC‑GCGGCGAGGGG‑AACAGGCCGCACTGCCCACCAATTTTCTGCTATCCTGCCCCCGCACAAAGGGGGCCGTATGCTAAACATCGTACTTTAc  >  1:1089662/1‑97 (MQ=255)                                                                                               |                                                                                                  CCCTCAGGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTC‑GCCCCTCCGGGGAGAGGGCC‑GGGGTGAGGGG‑AAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAC  >  NC_000913/3781047‑3781235

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: ‑