Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,333,776	0	G	T	39.6%	78.5 / 20.0	48	E23* (GAG→TAG)	ispB	octaprenyl diphosphate synthase
Reads supporting (aligned to +/- strand):  ref base G (11/18);  new base T (19/0);  total (30/18)
Fisher's exact test for biased strand distribution p-value = 6.72e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATTGCTGCCCTG  >  NC_000913/3333636‑3333925                                                                                                                                              |                                                                                                                                                       atatTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTa                                                                                                                                               <  1:692719/150‑1 (MQ=255)      ccTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGTGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTc‑c                                                                                                                                         <  1:632830/150‑1 (MQ=255)      ccTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAGCCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑Cg                                                                                                                                        <  1:799223/151‑1 (MQ=255)       cTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTA‑TAATGCACGCCTTGagcaggat                                                                                                                                                >  1:144979/1‑140 (MQ=255)            cATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAA‑AACGGCCATCCCTTCGGAGCTTTATTT‑CCGCGTcc                                                                                                                                  >  2:149743/1‑151 (MQ=255)              tAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTGA‑TGGGGGGATACTTTAGCCGCGTTATTT‑CCACGTcc                                                                                                                                  >  2:42716/1‑149 (MQ=255)                     tAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TTCGGAAAGACTTGAGCAGCCTAATTA‑CCACGGCCAACTGat                                                                                                                           >  1:826228/1‑149 (MQ=255)                       aGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAA‑TGAGGGAATCCTTTAGGAGCTTAATTT‑CGACGGCCCACAGatca                                                                                                                         >  2:617914/1‑149 (MQ=255)                              tttGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGGAA‑TTGGGGAAATCTTTAGCAGCTTAAATT‑CGACGCCCAACTGaacaaaaacgtat                                                                                                                >  1:631976/1‑143 (MQ=255)                               ttGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTa                                                                                                                 <  2:606751/149‑1 (MQ=255)                                 gTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCt                                                                                                             <  2:467957/151‑1 (MQ=255)                                  ttCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTA‑TGAGGCGAACCTTTAGGAACTTAATTT‑CGGCGTCCCACTGattaataaagtaagg                                                                                                              >  1:419087/1‑140 (MQ=255)                                    cacaGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTA‑TTAGGGAAACCTTTAGCAGCCTAATTT‑CGCCGCCCAACCGattaaacaaattaggtatt                                                                                                          >  1:1090556/1‑140 (MQ=255)                                     acaGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTA‑TGCAGGAAAACTTTATCAGCCTAATTT‑CGACGTCCCACTGATCAATCAATTAAGCTAtt                                                                                                          >  1:347239/1‑150 (MQ=255)                                           aGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGt                                                                                                   <  1:959358/151‑1 (MQ=255)                                               aaTCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTGAA‑TTAGGGAATCCTTTTGCCGCCTTATTCTCACCGCCCAAC‑GATCCATCCGTTAGGGTATTTCATcttttac                                                                                               >  1:66589/1‑145 (MQ=255)                                                     ggCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAgcggcggc                                                                                         <  2:39831/151‑1 (MQ=255)                                                         aaaaGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTa                                                                                     <  2:878118/151‑1 (MQ=255)                                                           aaGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTaaa                                                                                   <  2:862272/151‑1 (MQ=255)                                                           aaGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAA‑ATCGGGAAAACTTTAGCAGCTTTATTT‑CGCCGTCCCACTCATTAATAAATTAAGCTATTACAACGTCAGccgcggggggga                                                                                    >  2:1075862/1‑147 (MQ=255)                                                            aGCCCGGCTGTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACGGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAAc                                                                                  <  2:219051/151‑1 (MQ=255)                                                             gCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACg                                                                                 <  2:79848/151‑1 (MQ=255)                                                                   cTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTTA‑TGCGGGGAACCTTTAGCAGCTTTATTT‑CCACGTCCCACACATCAAACAATTAAGGTATTATATCGTCAGcggggggggggaaagtaat                                                                             >  2:383822/1‑139 (MQ=255)                                                                    ttttGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGGTTA‑TTGGGCAAACCTTTAGGAGCTTAATTT‑CGACGGCCCACTGATCAAACAATTTGGCGATTACATCGTCAGcggcggcggggaaaggattttt                                                                          >  2:1057900/1‑138 (MQ=255)                                                                    ttttGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTCA‑TTAGGCCATACTTTGGCAGGTTTATTC‑CGCCGGCCCAATTATCAAACAGATAAGGTATTACATCTTCAGCGGCGGCGGGaaaagcact                                                                             >  2:216715/1‑142 (MQ=255)                                                                       tGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAA‑TTAGGGAAACCCTTAGCAGCCTAAATT‑CGACGTCCAACAGATCAAACAAATAAGGTATTACATAGTCCGcggcgggggggaaagaattt                                                                            >  1:518845/1‑135 (MQ=255)                                                                          gATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGTTTA‑AGTGGCAATCCTTTAGCCGCTTAATTT‑CCACGTCCAACTGATCAAACCGTTTTGCTATTACATCGTCAGCGGCGGCGGGGAAAGTATTCTTCCgct                                                                     >  2:535553/1‑148 (MQ=255)                                                                               aTTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTAA‑TGTGGCGATCCCTTAGGAGCCTTATTT‑CGACGGCCCACTGATCAATCAGTTAGGGTATTACATCGTCCGCGGCGGCGGGGAAAGAATTTGTCCCCTGAtt                                                                 >  2:256992/1‑149 (MQ=255)                                                                                 ttAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGGGGTTA‑TTGGGCAAACCCTTAGCAGCTTAATTT‑CCACGTCCAACTGATCAATCAGTTTGGGTATTACATCGTCCGCGGCGGCGGGAAACGAATTTGTTCGCTGAtt                                                                 >  2:409109/1‑147 (MQ=255)                                                                                   aGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAATTGGGGCAA‑CCTTTAGGAGCCTTATTT‑CGACGGCCAACTGATCAAACAGTTTGGCTATTACATCATCAGCGGCGGCGGGGAAAGCATTTGTTCGATGATTGCt                                                              >  2:497752/1‑148 (MQ=255)                                                                                        aaaTCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGc                                                      <  1:755047/151‑1 (MQ=255)                                                                                            cAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCa                                                  <  1:290593/151‑1 (MQ=255)                                                                                              aTGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACg                                                <  1:804976/151‑1 (MQ=255)                                                                                                gAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAg                                              <  2:17122/151‑1 (MQ=255)                                                                                                   ttAACCGCGCAAGATATGGCGGGGGGTTA‑TGCGGCGATCCTTTTGCAGCTTAATTT‑CGACGTCCCACTGATCAAACAGTTAGGGTTTTTCATCGTCAGCGGGGGGGGGAAAAGGAATTGTCCCCTGATTTGTGTACTGGCTGcgc                                                 >  2:705220/1‑143 (MQ=255)                                                                                                     aaCCGCGCAAGATATGGCGGGGGTTTA‑TGCGGGAATCCTTTAGCAGGTTTATTT‑CCACGTCCCACCGATCAATCAATTAGGGTTTTTCATCGTCAGCGGCGGGGGGGAAAGGATTTGTCCGGTGATTTGTGTTCTGGGTGCGCGGGCTGt                                          >  2:365809/1‑150 (MQ=255)                                                                                                                     gCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATg                         <  2:145009/151‑1 (MQ=255)                                                                                                                             tAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTc                 >  2:766199/1‑151 (MQ=255)                                                                                                                             tAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTc                 >  2:657215/1‑151 (MQ=255)                                                                                                                                  gcagCAATCCTTGAGCAGCTTAATTC‑CGCCGTCCAACTGATCCATCAGATAGGCTGTTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGCTTGCTGGCCTGGCTGCACGGGCTGTTGGCTATGAGGTAAATGCGCATGTCAcc              >  1:581564/4‑150 (MQ=255)                                                                                                                                  gCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCAcc              <  1:1096013/150‑1 (MQ=255)                                                                                                                                  gCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCa             <  2:950917/151‑1 (MQ=255)                                                                                                                                       aaTCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATtgct        >  1:93077/1‑151 (MQ=255)                                                                                                                                        aTCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATtgctg       >  2:753447/1‑151 (MQ=255)                                                                                                                                            ttGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATTGCTGCCCt   >  2:491016/1‑151 (MQ=255)                                                                                                                                            ttGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATTGCTGCCCt   >  2:471783/1‑151 (MQ=255)                                                                                                                                            ttGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATTGCTGCCCt   >  2:352236/1‑151 (MQ=255)                                                                                                                                             tGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATTGCTGCCCTg  >  2:304180/1‑151 (MQ=255)                                                                                                                                              gAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCATGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATTGCTGCCCTg  <  2:256448/150‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                       ATATTCCTAACCATAAACCCTAAGTTGCCTTTGTTCACAGTAAGGTAATCGGGGCGAAAAGCCCGGCTTTTGCGATGAATTTAGAAAAAATCAATGAGTTAACCGCGCAAGATATGGCGGGTGTTAA‑TGCGGCAATCCTTGAGCAGCTTAATTC‑CGACGTCCAACTGATCAATCAGTTAGGCTATTACATCGTCAGCGGCGGCGGTAAACGTATTCGTCCGATGATTGCTGTACTGGCTGCACGAGCTGTTGGCTATGAGGGAAATGCGCATGTCACCATTGCTGCCCTG  >  NC_000913/3333636‑3333925

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑