Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,314,158	C→A	9.4%	R213S (CGC→AGC)	atoS →	sensory histidine kinase in two‑component regulatory system with AtoC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,314,158	0	C	A	9.4%	125.5 / 3.6	43	R213S (CGC→AGC)	atoS	sensory histidine kinase in two‑component regulatory system with AtoC
Reads supporting (aligned to +/- strand):  ref base C (20/19);  new base A (2/2);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.42e-01

ATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTGAGCGTAATGGTGAAATCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGATGGCGTCATTGCCATTGACCGCCAGGGTGATGTAACCACCATGAACCCAGCAGCAGAAGTTATCACTGGCTATCAACGC  >  CP009273/2313933‑2314418                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                                     aTGCGTTAAAATACCCCTTTAGTTTTTTCAGGCGGGAAGGTGCGCGTCTATATTTTTGATTCAATGCTCCACATTTAGCGTAATGGTGAAATCCTCGGCTATATCTGGGCCAATGTATTAACCGAAGATATTCGCCGCCAGTCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGc                                                                                                                                                                                                                     <  2:805938/275‑1 (MQ=255)                                              ggcgATATTTTGAATTCAATGCTCCCCATTGAGCGTAATGGTGAAATCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGcc                                                                                                                                                                                                                                                                   >  1:369449/1‑184 (MQ=255)                                                  atatTTTGAATTCAATGCTCCCCATTGAGCGTAATGGTGAAATCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTGGATTGTCCTTTTCTCCCGTCGCCTGAg                                                                                                                                                                                                                                                               <  2:369446/184‑1 (MQ=255)                                                   tatTTTGAATTCAATGCTTCCCATTGAGCGTAATGGTGAAATCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGCAATGGGGCaa                                                                                                                                                                    <  1:803247/274‑1 (MQ=255)                                                                               cGTAATGGTGAAATCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTACCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCAccc                                                                                                                                        >  1:469902/1‑274 (MQ=255)                                                                                  aaTGGTGAAATCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATCTTGATATCATCACCGATGGCCTCTCGActct                                                                                                                                                                                                                        >  1:254669/1‑191 (MQ=255)                                                                                         aaaTCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTACCACTCGATTAACAAAATTGCCAGATGAAATGGAGCAAATCAGTCAGAGTGTTAATAAACTGGCTNAGGCACTGctg                                                                                                                             >  2:67159/1‑273 (MQ=255)                                                                                            tCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGActct                                                                                                                                                                                                                        >  2:800083/1‑181 (MQ=255)                                                                                                cGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGca                                                                                                                                                                                                                    <  1:800089/181‑1 (MQ=255)                                                                                                            ggCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGGCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGCCTCTGGCACAAAATATTCACACTCTATTACCCCAATTGCCCGGTGAAAAGTGGCAAATCAGTCAACGTGATAATAACCTCGCCCAGGCACTGCGTGAAAngccggcccctaact                                                                                                          >  2:602084/1‑263 (MQ=255)                                                                                                                 aTGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAatat                                                                                                                                                                                                                                                      >  2:746534/1‑130 (MQ=255)                                                                                                                  tGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGcc                                                                                                                                                                                                                                                           >  1:340306/1‑124 (MQ=255)                                                                                                                  tGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGAGAAACGCGGACACTTNACGaaacat                                                                                                    >  2:327620/1‑270 (MQ=255)                                                                                                                    aaTTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCt                                                                                                                                             <  1:32679/232‑1 (MQ=255)                                                                                                                      ttAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAata                                                                                                                                                                                                                                                       <  2:340303/124‑1 (MQ=255)                                                                                                                                        cgccAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTc                                                                                                                                                                                                          >  1:768789/1‑151 (MQ=255)                                                                                                                                          ccAGGCCTGGAAAATGG‑ATGTGAGGATTACCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGTTGAAATGGGNCAACTCAATAAGAGTGTTAATAACCTCGCCAAGGCACTGCGTACAACGCGGACACTTAACGATCGGATTATTGAAAACGCTGCCGATGGc                                                                             >  1:595837/1‑274 (MQ=255)                                                                                                                                            aGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCAc                                                                                                                                                                                                      <  2:768783/151‑1 (MQ=255)                                                                                                                                               gatgctaaaTGGTATGTGTTGATTTTCTTTGTGTGCTACGTTGTTTTCATGATAAGCCTGCTGTTGTTTGTCCTTTTCTCCCGTCGCCTGAGCTCCAATATTGTTATCATCACCGATGTCCTCTCGACTCTGGCACAAAATATCCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATTAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCTCGAAACGCGGACCCTTAACGATCTGATTATTGAAATCGCTGCCGATGGCGTCa                                                                         <  2:595832/268‑1 (MQ=255)                                                                                                                                                           gaggtgAGGATAAACATTGTGATAACGGATGGTTTGCTGAAAACGCTGATGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCATCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCACGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGATGGCGTCATTGCCATTGACCg                                                            <  2:469899/272‑1 (MQ=255)                                                                                                                                                             tgtgAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAATCCTGCTGTTGATTGTCCTTTTCACCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACGCTGGCACAAAATATTCCCACTCGATTACCACAACTGCGAGGTGAAACGGGGCAAAtcagtta                                                                                                                                                            <  1:590991/177‑3 (MQ=255)                                                                                                                                                                          aTTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGATg                                                                               <  1:355915/241‑1 (MQ=255)                                                                                                                                                                                cTCACCGCTGGTTTGATGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCa                                                                                                                                       >  1:574699/1‑179 (MQ=255)                                                                                                                                                                                  cACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCAc                                                                                                                                                                                                                                          >  1:130344/1‑78 (MQ=255)                                                                                                                                                                                    ccGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCa                                                                                                                                   <  2:574696/179‑1 (MQ=255)                                                                                                                                                                                      gCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGAt                                                                                                                                                                                                                                      <  2:130343/78‑1 (MQ=255)                                                                                                                                                                                          gTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCAc                                                                                                                                                                                                                                          >  2:640268/1‑70 (MQ=255)                                                                                                                                                                                              gCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGAt                                                                                                                                                                                                                                      <  1:640274/70‑1 (MQ=255)                                                                                                                                                                                                       tctgctgTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGATGGCGTCATTGCCATTGACCGCCAGGGTGATGTAACCACCATGAACCCAGCAGCAGAAGTTATCa                <  1:683693/274‑1 (MQ=255)                                                                                                                                                                                                          gctgTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAAcgc                                                                                                                      >  1:284960/1‑170 (MQ=255)                                                                                                                                                                                                            tgTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAAAGCTGCCGATGGCGTCATTGCCATTGACCGCCAGGGTGATGTAac                                             >  1:120117/1‑241 (MQ=255)                                                                                                                                                                                                            tgTTGATTGTCCTTTTCTCCCGTAGCCTGAGCGCCAATATTGATATCTTCACCGa                                                                                                                                                                                                                                       >  1:764076/1‑55 (MQ=255)                                                                                                                                                                                                            tgTTGATTGTCCTTTTCTCCCGTAGCCTGAGCGCCAATATTGATATCATCACCGa                                                                                                                                                                                                                                       >  1:521498/1‑55 (MQ=255)                                                                                                                                                                                                              ttGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGac                                                                                                                  <  2:284957/170‑1 (MQ=255)                                                                                                                                                                                                                gATTGTCCTTTTCTCCCGTAGCCTGAGCGCCAATATTGATATCATCACCGATGGc                                                                                                                                                                                                                                   <  2:521495/55‑1 (MQ=255)                                                                                                                                                                                                                gATTGTCCTTTTCTCCCGTAGCCTGAGCGCCAATATTGATATCATCACCGATGGc                                                                                                                                                                                                                                   <  2:764070/55‑1 (MQ=255)                                                                                                                                                                                                                 aTTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAAcgc                                                                                                                      >  2:678327/1‑163 (MQ=255)                                                                                                                                                                                                                     tCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGac                                                                                                                  <  1:678333/163‑1 (MQ=255)                                                                                                                                                                                                                      ccTTTTTTCCCGTCGCCTGAGCGCCAATATGGTTATCATCACCGATGGCCTCTCGACTCTTGCACAAAATATTCCCACTCGATGACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAGGGCGTCATTGCCATTGACCGCCAGGGTGATGTAACCACCATGAACCCAGCAGCAGAAGTTATCACTGGCTATCAACGc  <  1:526271/274‑1 (MQ=255)                                                                                                                                                                                                                        ttttCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCa                                                                                                                                       >  2:746468/1‑139 (MQ=255)                                                                                                                                                                                                                            ctcCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCa                                                                                                                                   <  1:746474/139‑1 (MQ=255)                                                                                                                                                                                                                               ccGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTAcc                                                                                                                                                                                             >  2:281277/1‑78 (MQ=255)                                                                                                                                                                                                                               ccGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAAtca                                                                                                                                                                >  1:124108/1‑107 (MQ=255)                                                                                                                                                                                                                                   cGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACaa                                                                                                                                                                                         <  1:281280/78‑1 (MQ=255)                                                                                                                                                                                                                                   cGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAAtcagtca                                                                                                                                                            <  2:124107/107‑1 (MQ=255)                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                                     ATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTGAGCGTAATGGTGAAATCCTCGGCTATATCTGGGCCAATGAATTAACCGAAGATATTCGCCGCCAGGCCTGGAAAATGG‑ATGTGAGGATTATCATTGTGCTCACCGCTGGTTTGCTGATAAGCCTGCTGTTGATTGTCCTTTTCTCCCGTCGCCTGAGCGCCAATATTGATATCATCACCGATGGCCTCTCGACTCTGGCACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGATGGCGTCATTGCCATTGACCGCCAGGGTGATGTAACCACCATGAACCCAGCAGCAGAAGTTATCACTGGCTATCAACGC  >  CP009273/2313933‑2314418

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑