Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,171,882	0	C	G	43.8%	71.0 / 23.7	48	intergenic (+126/‑175)	rrfB/murB	5S ribosomal RNA of rrnB operon/UDP‑N‑acetylenolpyruvoylglucosamine reductase, FAD‑binding
Reads supporting (aligned to +/- strand):  ref base C (23/4);  new base G (0/21);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 5.78e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATCCCCCCACAGATACGGTAAACTAGCC  >  NC_000913/4171732‑4172031                                                                                                                                                         |                                                                                                                                                      gCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGccc                                                                                                                                                       <  2:105098/151‑1 (MQ=31) gCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGccc                                                                                                                                                       >  1:123124/1‑151 (MQ=31)  cGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATATGTTGTTTGTAGGTGAACGCAATCC‑GGAGTAGGATAAATCCGCCGGGAGAGGATTTGAAC‑GTTGCGAAGCAACGGCCCg                                                                                                                                                      >  2:243862/1‑151 (MQ=11)     gagTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCgg                                                                                                                                                     >  2:546697/1‑149 (MQ=31)         aGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGt                                                                                                                                                <  2:676878/150‑1 (MQ=31)         aGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGt                                                                                                                                                <  2:384091/150‑1 (MQ=31)         aGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGt                                                                                                                                                <  1:116637/150‑1 (MQ=31)               cTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGc                                                                                                                                         >  1:114910/1‑151 (MQ=31)                 gCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCa                                                                                                                                        <  1:146321/150‑1 (MQ=31)                       cATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGAcgcc                                                                                                                                 >  1:367967/1‑151 (MQ=31)                       cATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGAcgcc                                                                                                                                 >  1:743742/1‑151 (MQ=31)                        aTCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGAcgccc                                                                                                                                >  2:1352440/1‑151 (MQ=31)                             aaaaaaCGAAAGGCTCAGTCGAAAGACGGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAACCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCGGGAGGGTGGCGGGCAGGACGCCCGCCAt                                                                                                                           <  2:81653/149‑1 (MQ=9)                             aTAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCAt                                                                                                                           >  2:1026926/1‑151 (MQ=31)                             aTAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCAt                                                                                                                           >  2:545517/1‑151 (MQ=31)                              tAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCAt                                                                                                                           >  2:744855/1‑150 (MQ=31)                                       aGGCTCAGTCAAAAGACTGGGCTTTTCTTTTTATCTTTTTTTTGTGGGTGACCGCTCTCC‑TGAGAAGAAAAAACCCGCGGGGGGCGGATTTGAGC‑TTTGCGAAGCAAGGGCCGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAg                                                                                                                 <  1:1358992/151‑1 (MQ=2)                                         ccccagccaaaaGCCTGGCCTTTTTTTTTTATTTGTTTTTTGT‑GGGGAACCCCCCCCTTGAGAAGAAAAACCCCGCGGGGAGCGGATTTGACC‑GTTGCGAAGCACCGGCCGGGGGGGGGGGGGGCAGGACCCCCGCCATAAACTGCCAGGc                                                                                                               <  2:620307/142‑1 (MQ=2)                                            cAGTCGAAAGACTGGGCTTTTCTTTTTATTTTTTTTTTGTCGGTGAACGCTCTCT‑TGAGTGGGACAACCCCGCGGGGGGGGAATTTAAAC‑GTTGCGAAGCAACGGCCGGGGGGGTGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCa                                                                                                              <  1:274614/149‑1 (MQ=11)                                            cAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATc                                                                                                            >  2:119217/1‑151 (MQ=31)                                            cAGTCAAAAGCCTGGGCTTTTCTTTTTATCTTTTTTTTGTGGGTGACCCCCCTCC‑GGAGAAGGAAAAACCCGCGGGGGGGGGATTTAAAC‑GTTGCAAAGCACCGGCCGGGAGGGGGGCGGGCAGGCCGCCCGCCATAAACTGCCAGGCATc                                                                                                            <  1:250997/151‑1 (MQ=2)                                                cGAAAGCCTGGGCTTTTTTTTTTATCTGTTTTTTGTGGGTGACCGCTCTCT‑TGAGAAGGACAACTCCGCGGGGGGCGGATTTAAAC‑TTTGCAAAGCACCGGCCGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAAt                                                                                                        <  1:941422/151‑1 (MQ=2)                                                cGAAAGACTGGCCCTTTTTTTTTATTTTTTTTTTGTGGGTGACCCCTCTCC‑GGAGAAGAACAACCCCGCGGGGGGCGGATTTGAAC‑GTTGAGAAGCACCGGCCGGGGGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCaaag                                                                                                        <  2:384686/151‑2 (MQ=2)                                                 gAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAAtt                                                                                                       >  2:673781/1‑151 (MQ=31)                                                 aaaaGCCGGGGCTTTTTTTTTTTTTTTTTGTTTGTGGGTGAACGCTCTCT‑GGAGAAGAAAAACCCCGCGGGGGGCGGATTTGACC‑GTGGCGAAGCAGCGGCGGGGGGGGTGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAAtt                                                                                                       <  2:99242/150‑1 (MQ=2)                                                  aaaGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAAtt                                                                                                       >  2:826718/1‑150 (MQ=11)                                                                                       gaaaCGCTCTCT‑TGAGTGGAAAAAACCCGCGGGGGGGGGATTTGAAC‑TTTGCAAAGCACCGCCCGGGGGGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGtt                                                                 <  2:220182/149‑1 (MQ=11)                                                                                              cccccttgagagggACAACCCCGCGGGGGGGGGTTTGGACG‑GTTGAGAAGCAACGGCGGGGGGGGTGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACa                                                           <  2:1181902/139‑1 (MQ=11)                                                                                               ctcC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACaa                                                          >  1:512733/1‑150 (MQ=37)                                                                                                 cc‑TGAGTAGGAAAAACCCGCGGGGGGGGGATTTAAAC‑GTTGCGAAGCAACGGCCGGGGGGGGGGGGGGCGGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACaa                                                          <  1:830883/148‑1 (MQ=11)                                                                                                  c‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAActc                                                      >  1:998240/1‑151 (MQ=39)                                                                                                    tGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAActct                                                     >  1:1048064/1‑151 (MQ=40)                                                                                                     ggggagaaaaaccccgcggGGGGCGATTTTGAAT‑GTTGCGAAGCAGCGGCCGGGGGGGGGGGGGGCGGGCCCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCtt                                                    <  2:1210195/138‑1 (MQ=14)                                                                                                       gTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTcc                                                  >  1:828175/1‑151 (MQ=255)                                                                                                        gaGGACAACCCCG‑CGGGGGGGGGTTTGAACTGTGGAAAAGAACCGGCCGGGGGGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCt                                                 <  2:1062068/150‑1 (MQ=14)                                                                                                         ggaacaaccccgcggGGGGGGGATTTGAGC‑GTGGCGAAGCAGGGGCGGGGGGGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTg                                                <  2:858696/142‑1 (MQ=14)                                                                                                         aGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTg                                                >  2:1290899/1‑151 (MQ=255)                                                                                                                 cccgcggGGGGCGGTTTTAATC‑GTTGCAAAGCACCGGCGGGGGGGGTGGCGGGCAGGCCCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCata                                        <  2:1060083/150‑1 (MQ=17)                                                                                                                  ccgcggGGAGGGGATTGAAAC‑GTCGAAAAGCAGCGGCCGGGGGGGGGGCGGGCGGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCatat                                       <  2:113020/151‑1 (MQ=17)                                                                                                                   cgcggGGGGGGGATTTGACC‑GTGGCGAAGCAACGGCCGGGGGGGGGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATc                                      <  1:211864/151‑1 (MQ=17)                                                                                                                   cgcggGGAGGGGATTTGAAC‑GTTGCGAAGCAACGGCCGGGGGGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATc                                      <  1:1265552/151‑1 (MQ=17)                                                                                                                    gccgGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCt                                     >  1:881597/1‑151 (MQ=255)                                                                                                                           gCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGcc                              >  2:1054421/1‑151 (MQ=255)                                                                                                                              gATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATc                           >  1:322296/1‑151 (MQ=255)                                                                                                                                tttGATC‑GTTGCAAAGCAGCGGCCGGGGGGGGGGGGGGCAGGCCCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATcc                          <  2:1003766/150‑1 (MQ=18)                                                                                                                                 ttGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATcccc                        >  1:441687/1‑151 (MQ=255)                                                                                                                                    aaC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATcccccc                      >  1:688796/1‑150 (MQ=255)                                                                                                                                         ttGGGAAGCACCGGCCGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATCCCCCCACAg                  <  1:1369419/150‑1 (MQ=21)                                                                                                                                         ttGCGAAGCAAGGGCCGGGGGGGGGGGGGGAAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATCCCCCCACAg                  <  1:916201/150‑1 (MQ=21)                                                                                                                                          tGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATCCCCCcac                    >  1:674423/1‑147 (MQ=255)                                                                                                                                                        ccGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATCCCCCCACAGATACGGTAAACTAGcc  >  1:548430/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                      GCGAGAGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCC‑TGAGTAGGACAAATCCGCCGGGAGCGGATTTGAAC‑GTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCCATCCCCCCACAGATACGGTAAACTAGCC  >  NC_000913/4171732‑4172031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑