Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,850,007	0	G	A	45.5%	38.8 / 25.1	44	P44S (CCG→TCG)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  ref base G (22/2);  new base A (0/20);  total (22/22)
Fisher's exact test for biased strand distribution p-value = 2.62e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCC  >  NC_000913/3849858‑3850144                                                                                                                                                       |                                                                                                                                           cGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACgg                                                                                                                                            >  1:21606/1‑150 (MQ=255)                 atcatcAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGcc                                                                                                                           >  1:332028/1‑150 (MQ=255)                  tcatcaATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCat                                                                                                                         >  2:193277/1‑151 (MQ=255)                      caATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATc                                                                                                                      >  2:1104139/1‑150 (MQ=255)                            cGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGgcgc                                                                                                               >  1:588144/1‑151 (MQ=255)                                    gggTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAAcc                                                                                                         >  1:935599/1‑149 (MQ=255)                                      gTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAAcc                                                                                                         >  1:587058/1‑147 (MQ=255)                                           accgaccgCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAgg                                                                                                >  2:823994/1‑151 (MQ=255)                                             cgaccgCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCt                                                                                              >  2:674369/1‑151 (MQ=255)                                                ccgCCTGCGTTACCAATAAAACCAGCACCCCCCCCGCGCCCAGCAATCGGGGCCAGTACCCGCGCGGGCA‑TTGCAGCATTACCCCCAGACGCAGACAAAACGAAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGAt                                                                                           <  2:324982/151‑1 (MQ=255)                                                      gCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTcc                                                                                      >  1:617954/1‑150 (MQ=255)                                                        gTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                    >  1:331339/1‑150 (MQ=255)                                                             ccAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCa                                                                               >  2:882556/1‑150 (MQ=255)                                                               aaaaaaCCAGCACCCCCTCCGCCCCCAGAAATGGGGGCCAGTCCCCGCGGGGGCA‑TTGCAGCATTACCCCCAGACGCAGACAAAAGGAAAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGGTGCAGGCTGATACTCCACAGGCaa                                                                              <  1:876042/146‑1 (MQ=255)                                                                  aaaTCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAAcc                                                                          >  1:489717/1‑150 (MQ=255)                                                                  aaaCCAGCAGCCCCCCCGCCCCCAGCAATACGGGCAAGTACCCGCGCGGGCA‑TTGCACCATTACCCCCAGACGCAGCCAAAAGGAAAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAAc                                                                           <  2:435725/149‑1 (MQ=255)                                                                  aaaCCACCACCCACCCCGCCCCAAGAAACGCGGGCCAGTACCCGCGCGGGCA‑TTGCAACATTCCCCCCAGACGCAGACAAAAGAAAAATAC‑CAGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCaaa                                                                             <  1:541895/147‑1 (MQ=255)                                                                             ccccccGCGCCCAGCAATGGGGGCCGGTACCCGGGGGGGAA‑TTGCAGCATACCCCCCAGCCGCAAACAAAGCGGAAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAgaga                                                              <  1:815052/147‑1 (MQ=255)                                                                               ccccGCGCCAAGCAATGCGGGCCAGTCCCCGCGGGGGCA‑TGGCAGCATTACCCCCAGACGCAGCCAAAACGAAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGagaag                                                            <  2:454538/149‑1 (MQ=255)                                                                                cccccccccAGAAATACGGCCCAGTACCCGCGGGGGCA‑TTGCAGCATTACCCCCAGACGCAGACCAAACGAAAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGagaaga                                                           <  2:995022/145‑1 (MQ=255)                                                                                 ccGCCCCCACAAATGCGGCCAAGTCCCCGCGCGGGCA‑TGGCAGCATTACCCCAAGCCGAAGACAAAAGGAAAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGAt                                                          <  1:700889/151‑1 (MQ=255)                                                                                     gcCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCGGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaa                                                        >  1:255421/1‑149 (MQ=255)                                                                                            aaTGCGGGCCAGTACCCGCG‑GGGCATTTGCACCATCACCCCCAGGCGCAGACCAACCGAAAATAA‑AAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGc                                                  <  1:295608/148‑1 (MQ=255)                                                                                            aaTCCGGGCAAGTCCCCGCGGGGGAA‑TTGCAGCATAACCCCCAGACGCACACAAAACGAAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                     <  2:298631/145‑1 (MQ=255)                                                                                            aaTACGGCCAAGTCCCCGCGGGGGCT‑TGGCAGCATCCCCCCCAGACGAACACAAAAGGAAAAAAA‑ACGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaaa                                                    <  1:212213/146‑1 (MQ=255)                                                                                                cggggaagtccccGCGGGGGCA‑TTCCAGCATAGGCCCCAGACCAAGACAAAAGGAAAAAAA‑AACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAgg                                               <  2:1089164/136‑1 (MQ=255)                                                                                                 gggCCAGTACCCGCGCGGGCA‑TGGCAGCATTACCCCCAGCCGCAAACAAAACGAAAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATa                                          <  2:1088731/151‑1 (MQ=255)                                                                                                  ggCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATa                                          >  1:735143/1‑150 (MQ=255)                                                                                                  ggCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATa                                          >  1:294299/1‑150 (MQ=255)                                                                                                    ccAGTGCCCGCGGGGGAA‑ATGCAAATTAAGCCGCAGACGCAGACAAAACAAAAAAAA‑CAGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATa                                          <  1:869319/148‑1 (MQ=255)                                                                                                    ccAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACg                                       >  2:37889/1‑151 (MQ=255)                                                                                                        tATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTa                                    >  2:775133/1‑150 (MQ=255)                                                                                                           ccgggggggCA‑TGGCAGCATAACCCCCAGCCGCAGCCAAAAGGAAAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAAt                                  <  2:882102/143‑1 (MQ=255)                                                                                                           ccGCGCGGGCT‑TTGCAGCATTACCCCCAGACGCAGACAAAACGAAAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAAtt                                 <  2:624648/150‑1 (MQ=255)                                                                                                           ccGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAAtt                                 >  2:308726/1‑150 (MQ=255)                                                                                                                   gCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCggg                          >  1:165383/1‑149 (MQ=255)                                                                                                                          cagcaTTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaacaa                   >  2:602020/1‑150 (MQ=255)                                                                                                                          caccataccccccGGACGCAGACAAAACGAAAAAAA‑CACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaacaac                  <  1:361791/142‑1 (MQ=255)                                                                                                                            gcaTTACCCCCCGAAGGAGCCCAAACGAAAAAAA‑CACCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaacaa                   <  2:562176/148‑1 (MQ=255)                                                                                                                               ttACCCCCAGACGCAGACAAAACGAAAAAAA‑CGCCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaac                     <  1:528324/143‑1 (MQ=255)                                                                                                                                   ccccGGACGCAGA‑CAAACGGAAAAAACCAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCtt             <  2:515049/147‑1 (MQ=255)                                                                                                                                       acacaaacccaaaaCGAAAATAA‑AAACACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCAcc      <  1:990380/139‑1 (MQ=255)                                                                                                                                        gACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCAcc      >  2:402973/1‑149 (MQ=255)                                                                                                                                           gCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGcc  >  2:327139/1‑150 (MQ=255)                                                                                                                                                  aaaCGAAAAAAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCa     <  1:1044841/140‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                           CGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAACCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCA‑TTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAA‑CAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCC  >  NC_000913/3849858‑3850144

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑