Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,850,007	0	G	A	45.1%	54.3 / 23.3	51	P44S (CCG→TCG)	uhpB	sensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  ref base G (25/3);  new base A (0/23);  total (25/26)
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

ACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCA  >  NC_000913/3849857‑3850148                                                                                                                                                            |                                                                                                                                              aCGTCAGTAAACTGCCGTTCACAAAAAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACg‑g                                                                                                                                               <  2:739508/151‑1 (MQ=255) aCGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACg‑g                                                                                                                                               <  1:606604/151‑1 (MQ=255)   gTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑Ga                                                                                                                                              >  1:505109/1‑150 (MQ=255)      aGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAC‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATa                                                                                                                                          <  1:757609/151‑1 (MQ=255)         aaaCTACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATa                                                                                                                                          >  2:915723/1‑148 (MQ=255)           aCTACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAg                                                                                                                                      >  1:496015/1‑150 (MQ=255)             tACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCAc                                                                                                                                   >  2:1017391/1‑151 (MQ=255)             tACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCAc                                                                                                                                   >  1:71426/1‑151 (MQ=255)               ccGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCg                                                                                                                                 >  1:1005261/1‑151 (MQ=255)                             cGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGgcgc                                                                                                                   >  2:528439/1‑151 (MQ=255)                              ggAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCt                                                                                                                  >  1:164350/1‑151 (MQ=255)                                   aagggTTAAACCCCGCCCGCCTGCGTGGGCC‑GGTAAATCGGCCCCCCCCCCGCCCCCAGCAAAGCGGGCCA‑GTATCCGCGGGGGATTCGCAGATTAAGCCCGGGACGAAAACAAAACG‑AAAATAACACCGCCGCCATATCAGGGCGCTCa                                                                                                                <  2:463827/148‑1 (MQ=255)                                    tGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAAcc                                                                                                             >  2:845183/1‑150 (MQ=255)                                          aaa‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGc                                                                                                       >  1:731580/1‑150 (MQ=255)                                                  cccgCCTGCGTTAGCA‑AAAAAATCAGCACCCCCCCCGCGCCCAGCAATACGGGCCA‑GTACCCGCGCGGGCATGGCAGCATTAGCCCCAGACGAAGACAAAAGG‑AAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCt                                                                                                  <  1:818338/148‑1 (MQ=255)                                                   ccgCTTGGGTTAGCA‑AAAAACTCACCACCCGCCCCCCGCCCAGCAACCGGGGCCA‑GTCCCGGCGCGGGCATAGAAACAGCCGCCCCAGACG‑AAACGAAAAGAAAAAAAAAAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCt                                                                                                  <  1:142541/148‑1 (MQ=255)                                                    ccccgggcttAGCCAAGAAAACCACCACCCCCCCCCCGCCAAGAAAGCCGGCCCA‑GTACCCGCGCGGGATTGGCAGCATTACCCCCGGCCGCAGCCCAAGCG‑AAAATAACGGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGc                                                                                                   <  2:766031/139‑1 (MQ=255)                                                     gCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATAc                                                                                             >  1:158983/1‑151 (MQ=255)                                                      ccTGCGTTGGCA‑AGAAAACCAGCGCCCCCCCCGCGCCCAGCAAACCGGGCCA‑GTACCCGCGCGGGAATTGCAGCATTAGCCCCAGACGCAGCCAAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACt                                                                                            <  1:202765/151‑1 (MQ=255)                                                            ttAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCcac                                                                                        >  1:370902/1‑149 (MQ=255)                                                                 caagaaaaCCAGCACCCCCCCCGCCCCCAGCAACGCGGGCCA‑GTACCCGCGCGGGCATTGCAGCATTACCCCCAGACGCAGACAAAAGG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCaa                                                                                  <  1:51525/146‑1 (MQ=255)                                                                       aaTCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCAt                                                                            >  1:766408/1‑151 (MQ=255)                                                                       aaTCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCAt                                                                            >  1:319313/1‑151 (MQ=255)                                                                                cccccccGCGCCCACCAAGCCGGGCAA‑TTACCCGCGGGGGCATTGCACCATTCGCCCCAGCCGAAGACAAAACG‑AAAAAAACACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCag                                                                     <  2:726489/144‑1 (MQ=255)                                                                                  aCTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTAAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCagag                                                                   >  2:1058567/1‑149 (MQ=255)                                                                                   cTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAgaga                                                                  >  2:298027/1‑149 (MQ=255)                                                                                    tCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAgaga                                                                  >  2:751021/1‑148 (MQ=255)                                                                                    cccGCCCCCAGCAAGACGGGCAA‑GTACCCGCGGGGGCATTGCAGCATTCCCCCCAGCCGCAGACAAAACG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGagaaga                                                               <  1:28288/150‑1 (MQ=255)                                                                                      cgctccaagaaagaggggCCA‑GTACCCGCGCGGGCATTGCCGCATTCCCCCCCGACGAAACAAAAACG‑AAAATAACAGCTCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATa                                                             <  2:687151/136‑1 (MQ=255)                                                                                      cgcgCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGAt                                                              >  1:277204/1‑150 (MQ=255)                                                                                      cccccccAACAAAACGGGGCAGGTTCCCGGGCGGCCCTGGCAACATCACCCCCACACCCAAACAAAAGG‑AAAAAAAAACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGAt                                                              <  2:453267/147‑1 (MQ=255)                                                                                        cccccAACAATACGGCCCA‑GTACCCGCGCGGGAATTGCACCATTACCCCCAGACGCACCCCAAACG‑AAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATaaa                                                           <  1:650580/149‑1 (MQ=255)                                                                                        ccccaagaaaagcGGGCAA‑TTATCCGCGCGGGCATGGAAGAATAACCCCAAGACGCAAACAAAAGG‑AAAATACCACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATa                                                             <  1:427096/137‑1 (MQ=255)                                                                                                aatcggggCCA‑GTCCCCGGGCGGGCTTTGCAGCATTACCCCCAGACGCAGACCAAACG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAg                                                    <  1:626813/145‑1 (MQ=255)                                                                                                aatcggggCCA‑GTATCCGCGCGGGCATTGCAGCATTACCCCCAGACGAAGACAAAACG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAg                                                    <  1:1025972/145‑1 (MQ=255)                                                                                                aaggcGGGCCA‑GTACCCGCGGGGGCATTGCAGCATTACCCCCAGACGAAGAACAAACA‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAg                                                       <  2:230598/143‑1 (MQ=255)                                                                                                    cGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAAt                                               >  2:552851/1‑151 (MQ=255)                                                                                                       ggcaggTATCCGGGCGGGCATTGCAGCATTACCCCCAGACGCAGACAAACAG‑AAAAAAACACCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATaa                                             <  1:49092/146‑1 (MQ=255)                                                                                                                ccGCGCGGGCATTGCAGCTTGACCCCCAGACGCAAACAAAACG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTa                                        <  2:1042367/147‑1 (MQ=255)                                                                                                                     cgGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCgg                               >  2:398986/1‑151 (MQ=255)                                                                                                                       ggCATGGCAGCATAACCCACACACACAAAAAAAAGG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGga                             <  2:997791/151‑1 (MQ=255)                                                                                                                            tGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGaac                         >  2:1066242/1‑150 (MQ=255)                                                                                                                                  aTTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCt                  >  2:78261/1‑151 (MQ=255)                                                                                                                                   ttAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCAACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCt                  >  2:931120/1‑150 (MQ=255)                                                                                                                                       cccgAGACGCAGACAAAACG‑AAAAAACCACCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCt                  <  1:917134/146‑1 (MQ=255)                                                                                                                                       ccccAGCCGCAGACCAAACG‑AAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTc                   <  1:842291/145‑1 (MQ=255)                                                                                                                                       cccaAGACGAACACAAAAGG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCtt                 <  1:356506/147‑1 (MQ=255)                                                                                                                                          cAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCAcc          >  1:455679/1‑151 (MQ=255)                                                                                                                                            aaagcaacccAAACG‑AAAATAGCTGCTCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTtca               <  1:554668/136‑1 (MQ=255)                                                                                                                                                 acacaaaaCG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCa         <  2:319248/140‑1 (MQ=255)                                                                                                                                                 aGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATc   >  1:493338/1‑151 (MQ=255)                                                                                                                                                    caaaaCG‑AAAAAAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCa  <  1:413054/147‑1 (MQ=255)                                                                                                                                                      aaaGG‑GAAAAAACAGCCCCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGcc      <  2:835690/143‑1 (MQ=255)                                                                                                                                                            |                                                                                                                                              ACGTCAGTAAACTACCGATCATCAATAACGGAAAATGGGTTAAA‑‑CCGACCGCCTGCGTTAGCC‑AGTAAATCAGCAGCCACTCCGCGCCCAGCAATACGGGCCA‑GTATCCGCGCGGGCATTGCAGCATTAGCCCCAGACGCAGACCAAACG‑GAAATAACAGCACCGCCATATCAGGGCGCTCAACCAGATGCAGGCTGATACTCCACAGGCAAAACCATGCGGCAGAGAAGATAAAAAAGCAGGCAATAACGGTAATTAAGCGGGAGAACAACGTCTTCATCACCAGCCATCA  >  NC_000913/3849857‑3850148

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: ‑