Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,850,0070GA43.1% 59.7 / 23.1 51P44S (CCG→TCG) uhpBsensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  ref base G (26/3);  new base A (0/22);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.47e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCA  >  NC_000913/3849860‑3850145
                                                                                                                                                    |                                                                                                                                          
tCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGaa                                                                                                                                          >  1:942502/1‑150 (MQ=255)
  aGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAAt                                                                                                                                        >  1:473775/1‑150 (MQ=255)
      aaCTACCGATCATCAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAg                                                                                                                                   <  2:849161/151‑1 (MQ=255)
         tACCGATCATCAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCa                                                                                                                                 >  1:194222/1‑150 (MQ=255)
           ccGATCATCAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACATCACCg                                                                                                                              >  2:701946/1‑151 (MQ=255)
             gATCATCAATAACGGAAAATGGGTTAAC‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGcc                                                                                                                            <  2:280976/151‑1 (MQ=255)
              atcatcAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGcc                                                                                                                            >  1:962136/1‑150 (MQ=255)
                catcaATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCat                                                                                                                          >  1:500718/1‑150 (MQ=255)
                       aaCGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGAGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAggg                                                                                                                   >  1:1004489/1‑150 (MQ=255)
                            aaaaTGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCt                                                                                                               >  1:953211/1‑149 (MQ=255)
                              aaggggTTAAACCCGCCCGCCTGGGTGACCAAAAAAACCAGCCCCCCCCCCCCCCCCAACAACACGGGCCAGTCCCCGCGCGGGCATGGCAGCATTCCCCCCAGACCCAGCCCAAACAAAAATACCAGCCCCGCCATATCAGGGCGCTCaa                                                                                                            <  1:280198/148‑1 (MQ=255)
                                          ccgaccgCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGAACCGCCATATCAGGGCGCTCAACCAGATGCAGGc                                                                                                >  2:98774/1‑151 (MQ=255)
                                             accgCCTGCGTTAGCCAGTAAATCGGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTg                                                                                              >  2:506778/1‑150 (MQ=255)
                                              cccccTGCTTTAGCAAGAAAACCAGCACCCCCCCCGCGCCCAGAAATGGGGGCCATTACCCGCGGGGGATTTGCAGCTTTACCCCCAGACGCAGACAAAAGGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTg                                                                                              <  2:830047/146‑1 (MQ=255)
                                               cgCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGAt                                                                                            >  1:657131/1‑150 (MQ=255)
                                                   tGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTcc                                                                                       >  2:458588/1‑151 (MQ=255)
                                                    gCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATa                                                                                           >  2:720076/1‑146 (MQ=255)
                                                     cGTGAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                     >  1:322007/1‑151 (MQ=255)
                                                      gTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                     >  2:830531/1‑150 (MQ=255)
                                                           caagaaaaaCAGCCGCCCCCCCCCGCCCACAAACAGGGGCCAGTCCCCGCGCGGGCATTGCAGAATGACCCCCACCCGCAGAAAAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCa                                                                                <  1:192313/145‑1 (MQ=255)
                                                                aaaccaccaccccccccGCCCCAAGCAATCGGGCCCAGTCCCCGCGCGGGTATTGCAGCATCCCCCCCAGCCGCAGACAAAACGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCa                                                                          <  2:901123/136‑1 (MQ=255)
                                                                    cagcagCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCg                                                                      >  1:432505/1‑151 (MQ=255)
                                                                    cagcagCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCg                                                                      >  1:362371/1‑151 (MQ=255)
                                                                      gcagcCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGc                                                                    >  1:150788/1‑151 (MQ=255)
                                                                         ccccccccGCCCCCAGAAACAGGGCCGATTACCCGCGGGGCCATGCCACCATTGCCCCCGGACACAGACAAAAGGAAAAAAAAAGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCaga                                                                 <  1:122721/145‑1 (MQ=255)
                                                                          cccccccGCCCCCACAAATGCGGCCCAGTCCCCGGGGGGCAATTGCAGAATTACCCCCAGCCCAACACAAAACGAAAAAAACACCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCag                                                                  <  1:819081/144‑1 (MQ=255)
                                                                          cccccccGCCCCCAAAAATGCGGGCCAGTCCCCGCGGGGGCATTGCAGCTTTACCCCCAGACGCAAACAAAAGGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCgg                                                                     <  2:1027778/141‑1 (MQ=255)
                                                                          cccccccGCCCCAAGAAATGCGGCCAAGTACCCGCGGGGGCATTGAAGCATTCCCCCAAGCCGCAAACAAAAGGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCagag                                                                <  2:727335/146‑1 (MQ=255)
                                                                             cTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAgaga                                                               >  1:1014249/1‑149 (MQ=255)
                                                                                  cccccagaaaggggggCCAGTACCCGCGGGGGAATCGCAGTATAACCCCAAGCCGCAGACAAAAGGAAAATAAAAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaa                                                        <  2:59005/138‑1 (MQ=255)
                                                                                     ccAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaaaa                                                      >  2:643263/1‑150 (MQ=255)
                                                                                       agaaaTACGGGCCAGTACCCGCGCGGGCTTGGCAGCATTCCCCCCAGACGCAGACAAAAGGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaa                                                        <  2:1015758/143‑1 (MQ=255)
                                                                                       aGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGc                                                   >  1:807836/1‑151 (MQ=255)
                                                                                          aagaggggCCAGTCCCCGCGGGGGATTTGCAGCATTACCCCCAGCCGAAAACAAAACGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGc                                                   <  2:205895/143‑1 (MQ=255)
                                                                                          aaTGCGGGCCAGTACCCGGGCGGCAAGTGCAGCATTCGCCCCAGACGCACACAAAAGGAAAATACCACCGCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAg                                                    <  2:942868/147‑1 (MQ=255)
                                                                                               gggCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAAt                                            >  1:228199/1‑150 (MQ=255)
                                                                                               gggCCAGTACCCGCGGGGGCATTGCAGCATTACCCCCAGCCGCAGACAAAACGAAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCa                                              <  2:352238/148‑1 (MQ=255)
                                                                                               ggcccAGTCCCCGCGGGGGCATCGCAACATTACCCCCAGACGAACCAAAAACGAAAATAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCaa                                             <  2:450835/146‑1 (MQ=255)
                                                                                                    agtcccggcgggGGAATTGCAGCTTTACCCCCAGACGCACCCAAAACGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACg                                        <  2:860988/142‑1 (MQ=255)
                                                                                                    agtccccGCGGGGGCATGCCAGCATCCCCCCCAGACGCAAACAAAACGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACg                                        <  2:459591/144‑1 (MQ=255)
                                                                                                      tacccGCGCGGGCATCGCACCATTCCCCCCAGCCGCAGACAAAACGAAAAAAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACgg                                       <  2:594170/145‑1 (MQ=255)
                                                                                                         ccGCGCGGGCATGGCAGCATACCCCCCAGACGCAAACAAAAGGAAAAAACCACCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTa                                 <  1:160375/151‑1 (MQ=255)
                                                                                                          cgcgcgGCAATTGCAGCATTCCCCCCAGACGCAGACAAAAGGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTaa                                    <  2:428547/147‑1 (MQ=255)
                                                                                                           gcgcgGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAAtt                                  >  1:666036/1‑148 (MQ=255)
                                                                                                                        agcaTTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACg                  >  1:1017856/1‑151 (MQ=255)
                                                                                                                            tcacccccAGACGCAGCCAAAACGAAAAAAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaacaac                   <  2:1036945/142‑1 (MQ=255)
                                                                                                                              aGCCCCCGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGCGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAATCAGGCAATAACGGTAATTAAGCGGGAGAACAACGGCTtc             >  1:309658/1‑150 (MQ=255)
                                                                                                                                ccccAGACGCAAACCAAACGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCtt              <  2:753896/147‑1 (MQ=255)
                                                                                                                                       cgaaaaCCAAACGAAAACAACACCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGcc   <  1:747331/146‑1 (MQ=255)
                                                                                                                                       cGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAACAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGcc   >  1:540379/1‑151 (MQ=255)
                                                                                                                                          aGACAAAAGGAAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCa  <  2:474007/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                          
TCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑CCGACCGCCTGCGTTAGCCAGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCAGTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACGGAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCA  >  NC_000913/3849860‑3850145

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: ‑