Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,850,007	0	G	A	40.0%	53.0 / 18.7	45	P44S (CCG→TCG)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  ref base G (20/7);  new base A (0/18);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 2.97e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01

AGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAAC  >  NC_000913/3849862‑3850151                                                                                                                                                   |                                                                                                                                                    aGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAAt                                                                                                                                                >  2:1001129/1‑150 (MQ=255) aGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAAt                                                                                                                                                >  1:337271/1‑150 (MQ=255)   tAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑c                                                                                                                                            >  1:563247/1‑151 (MQ=255)   tAAACTACCGATCATCAATAACGGAAAAGGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATaa                                                                                                                                              <  1:33432/150‑1 (MQ=255)    aaaCTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑c                                                                                                                                            <  2:748336/150‑1 (MQ=255)    aaaCTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑c                                                                                                                                            <  1:42944/150‑1 (MQ=255)         aCCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑cc                                                                                                                                     >  2:647564/1‑151 (MQ=255)          ccGATCATCAATAACGGAAAAGGGTTGAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑cc                                                                                                                                     <  1:331754/150‑1 (MQ=255)             atcatcAATAACGAAAAATGGGTTAACCCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGc                                                                                                                                   <  2:882936/149‑1 (MQ=255)                 tcaATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATc                                                                                                                             >  1:855302/1‑151 (MQ=255)                     tAACGGAAAATGGGGTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAggg                                                                                                                         >  1:800619/1‑151 (MQ=255)                       aCGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGgcg                                                                                                                       >  2:857292/1‑151 (MQ=255)                                gggaaacaccccccgccgGGGTAAGCAAGAAAAACACCACCCCCCCCGCGCCCAACAAGAGGGGCCAGCACCCGCGCGGGCATGGCAGCATAGCCCCCGGCCGCAGCCCAAACG‑A‑AAAAAA‑CACCC‑CCGCCATATCAGGGCGCTCAAcc                                                                                                                <  1:286772/137‑1 (MQ=255)                                       accgaccgCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAgg                                                                                                       >  2:877020/1‑151 (MQ=255)                                             cgCCGGCTTTAGCAAGAAAACCACCACCCCCCCCGCCCCCAGAAATGGGGCCCAGTCCCCGCGCGGGCATGAAAGCTTTACCCCCAGACGCACCCAAAACG‑A‑AAAAAA‑CAGCC‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATa                                                                                                 <  2:807456/151‑1 (MQ=255)                                              gCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATAc                                                                                                >  1:313649/1‑151 (MQ=255)                                                   cGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                           >  1:978363/1‑151 (MQ=255)                                                          cAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCaa                                                                                     >  2:141999/1‑150 (MQ=255)                                                            gTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAAc                                                                                  >  1:928098/1‑151 (MQ=255)                                                             aaaaTCACCACCCCCCCCGCGCCCAAAAAAGCGGGCCATTCCCCGCGCGGTCATTGCACCATTCCCCCCAGCCGCA‑ACCAAAAGAA‑AAAAAA‑CACCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                           <  2:135582/140‑1 (MQ=255)                                                                   agcagcCACTCTGCGTCCAGCAATACGGGCCAGTATTTGTGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACTAGATGCAGGCTGATACTCCACAGGCAAAACTATGCgg                                                                           >  1:97141/1‑151 (MQ=255)                                                                     cgccccccccccccccAGCAACGGGGGCCAGTACCCGCGCGGTCTTTGCAGCATTCCCCCCAGACGCAGACCAAACG‑A‑AAAAAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGTgg                                                                           <  2:627452/136‑1 (MQ=255)                                                                     ccccccccccGCCCCAAGCAACGGGGGCCAGTACCCGCGCGGGCATCCCAGCATTACCCCCCGCCCCACACAAAACG‑A‑AATTAC‑CCCCC‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCg                                                                            <  1:877905/140‑1 (MQ=255)                                                                        cccccccGCCCCCAGAAACAGGGCCCAGTACCCGCGGGGGCATTGCACCATTACCCCCAGACGCAGACAAAACG‑A‑AAAAAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCgg                                                                           <  2:627465/141‑1 (MQ=255)                                                                          aCTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAgaga                                                                     >  1:475462/1‑150 (MQ=255)                                                                                    cAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                            >  1:137583/1‑149 (MQ=255)                                                                                        aaggggggACAGTACCCGGGCGGGCATAGCAGAATTACCCCCAGACGCAAACAAAAGG‑A‑AAAAAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAg                                                          <  1:922777/142‑1 (MQ=255)                                                                                        aaggcGGCCCAGTCCCCGGGGGGGAATTGCACATTTACCCCCAGCCGAAAACAAAAGG‑A‑AAAAAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGc                                                         <  2:813127/144‑1 (MQ=255)                                                                                        aaTGCGCGCCAGTCCCCGGGGGGGCATGGCACCATTACCCCCAGAC‑AAAACAAAAAG‑G‑AAAAAACCAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAgg                                                      <  1:696519/151‑1 (MQ=255)                                                                                        aaTACGGGCGAGTCCCCGGGCGGATATTCCACCATAACCCCCAGCCGCAGACCAAACA‑A‑AAAAAA‑CACAA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                            <  2:108178/145‑1 (MQ=255)                                                                                             gggCCAGTACCCGGGGGGGAATTGCCGCATTCGCCCCGGACGCAACCAAAACG‑A‑AAAAAC‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaa                                                               <  2:862951/137‑1 (MQ=255)                                                                                                cgattccccGCGCGGGCAGGACACCATCGCCCCCAGACGAACACCAACGA‑A‑AAACAA‑CATCC‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACg                                              <  1:221012/144‑1 (MQ=255)                                                                                                 cagtccccGCGCGGCCATAGCACCATGACCCCCAGCCCAACACAAAAAG‑A‑AAAAAA‑CAGCC‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATa                                                 <  1:770419/141‑1 (MQ=255)                                                                                                 cAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACgg                                             >  1:139997/1‑151 (MQ=255)                                                                                                  aGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACgg                                             >  1:41979/1‑150 (MQ=255)                                                                                                     acccGCGCGGCAATTCAAGCTTCACCCCCAAACGAAGACAAAAAG‑A‑AAAAAA‑CCGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGt                                            <  1:585761/146‑1 (MQ=255)                                                                                                           gcgGGCATTGCAGCATTACCCCCAGACGCAGACAAAAGG‑A‑AAAAAA‑CACCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTaa                                      <  2:546411/148‑1 (MQ=255)                                                                                                                   cacataattccccccAAACGCATCCCAACCG‑A‑AAATAA‑CATCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGgaga                              <  2:402240/137‑1 (MQ=255)                                                                                                                      agcaTTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACg                        >  2:499827/1‑151 (MQ=255)                                                                                                                       gcaTTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGt                       >  1:785533/1‑151 (MQ=255)                                                                                                                         cagaggcccacgagCAGAACAAAGA‑A‑AAAAAA‑CCGCATCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGt                       <  2:334991/137‑1 (MQ=255)                                                                                                                          tcacccccAGCCGCAAACCAAACG‑A‑AAACCC‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCt                     <  2:948746/146‑1 (MQ=255)                                                                                                                                  aGACGCAGACCAAACG‑A‑AAAAAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCAc              <  2:30967/149‑1 (MQ=255)                                                                                                                                    gacgaaaCCAAAAG‑GAAAAAAA‑CACCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGgaga                              <  1:944804/126‑1 (MQ=255)                                                                                                                                             aaaCG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAAc  >  1:378442/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                    AGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑G‑AAATAA‑CAGCA‑CCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCAAAC  >  NC_000913/3849862‑3850151

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑