Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,349,969	A→G	7.4%	T156A (ACC→GCC)	PP_2945 →	two‑component system sensor histidine kinase/response regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,349,969	0	A	G	7.4%	152.0 / 2.6	55	T156A (ACC→GCC)	PP_2945	two‑component system sensor histidine kinase/response regulator
Reads supporting (aligned to +/- strand):  ref base A (28/22);  new base G (2/2);  total (31/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.53e-01

GCTGTTGCAGGTAGTCGTCTGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAGCGCAAGCAGCTGGAAAGCCAACTGGTG  >  NC_002947/3349824‑3350115                                                                                                                                                   |                                                                                                                                                   gCTGTTGCAGGTAGTCGTCTGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCCGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGTCAGCAAGGTGCTGGCCa                                                                                                                                                 >  3:315878/1‑149 (MQ=255)       gCAGGTAGTCGTCTGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCCGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGTCAGCAAGGTGCTGGCCatttgc                                                                                                                                            <  4:315878/148‑6 (MQ=255)       gCAGGTAGTCGTCTGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCGCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTgg                                                                                                                                            <  8:191631/148‑1 (MQ=255)         aGGTAGTCGTCTGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGa                                                                                                                                          >  3:9795/1‑148 (MQ=255)                 gtcTGCACTGCCTACTCGGACTATTCCTGGGATGAGATGCTCGACCGGCTGCAGGACCACGATCCCTTGCT‑GATAATGAAAAAACCGTTCGACAAAATCGAGGTCCAGCAAATGGCAAGCACCTTGCTGACAAAGTGTGAAATGAcac                                                                                                                                  >  7:189918/1‑146 (MQ=255)                    tGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGACAGCAAGGTGCTGGCCatttgct                                                                                                                                           <  4:54706/136‑7 (MQ=255)                    tGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGACAGCAAGGTGCTGGCCatttgct                                                                                                                                           >  3:54706/1‑130 (MQ=255)                        cTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGc                                                                                                                           >  4:17473/1‑148 (MQ=255)                        cTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGAACGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGc                                                                                                                           >  4:21999/1‑148 (MQ=255)                           ccTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTc                                                                                                                        <  1:284227/148‑1 (MQ=255)                             tACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGt                                                                                                                                              >  8:265009/1‑124 (MQ=255)                             tACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGt                                                                                                                                              <  7:265009/124‑1 (MQ=255)                              aCTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCt                                                                                                                     >  8:285170/1‑148 (MQ=255)                                tCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGa                                                                                                                   >  2:167581/1‑148 (MQ=255)                                  ggACTATTCCTGGGATGAGTTGCTCGACCGGCTGCCGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGCCAACATCGAGGTCCAGCAAATGGCCAGCACCGTGCTGACCAAGTGGGAAATGACCCAACGAGACTCGCTGaaaa                                                                                                                >  6:243079/1‑149 (MQ=255)                                  ggACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGaaaa                                                                                                                >  6:143382/1‑149 (MQ=255)                                   gACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAAt                                                                                                               <  4:9795/149‑1 (MQ=255)                                           cTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GCTCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGTAAATGCACCAGc                                                                                                       >  3:271322/1‑149 (MQ=255)                                           cTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCCGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGc                                                                                                       >  7:134430/1‑149 (MQ=255)                                           cTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAg                                                                                                        <  8:117527/148‑1 (MQ=255)                                           cTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGc                                                                                                       >  4:121747/1‑149 (MQ=255)                                                 tGAGTTGCTCGACCGGCTGCAGGCCCACTATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCATCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAAc                                                                                                 <  7:110630/149‑1 (MQ=255)                                                       gCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCgg                                                                                            <  3:17473/148‑1 (MQ=255)                                                       gCTCGAACGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCgg                                                                                            <  3:21999/148‑1 (MQ=255)                                                         tCGACCGGCTGCAGGCCCACGATCGCTTGCTAGATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACATTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCggg                                                                                           >  1:208450/1‑148 (MQ=255)                                                           gACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGCCGAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTa                                                                                         >  5:263045/1‑147 (MQ=255)                                                           gACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTa                                                                                         >  4:139355/1‑147 (MQ=255)                                                             ccGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAgc                                                                                     <  3:121747/149‑1 (MQ=255)                                                                         ccACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAg                                                                          >  3:47771/1‑148 (MQ=255)                                                                            cGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAAc                                                                      >  6:340072/1‑149 (MQ=255)                                                                             gATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACt                                                                     >  5:21839/1‑149 (MQ=255)                                                                             gATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACt                                                                     >  3:107269/1‑149 (MQ=255)                                                                             gATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACt                                                                     >  5:26819/1‑149 (MQ=255)                                                                                 gCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGAc                                                                  <  5:143382/148‑1 (MQ=255)                                                                                  cTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGAcc                                                                 >  5:338051/1‑148 (MQ=255)                                                                                   ttGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGAcc                                                                 >  7:86115/1‑147 (MQ=255)                                                                                     gCT‑GATCCTGATAAAACCTTTCGACAACATCGAGGTCCAGCAAATGGCAAGCACCTTGCTTACCAAGTGGGAAATGACCCTACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCa                                                               <  8:189918/147‑1 (MQ=255)                                                                                      cT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGc                                                            >  5:224895/1‑149 (MQ=255)                                                                                          aTCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAg                                                         >  7:97745/1‑149 (MQ=255)                                                                                              tGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAg                                                     >  2:175546/1‑149 (MQ=255)                                                                                                 aaaaaCCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGgcg                                                  <  4:107269/149‑1 (MQ=255)                                                                                                 aaaaaCCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGgcg                                                  <  4:47771/149‑1 (MQ=255)                                                                                                  aaaaCCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGgcgc                                                 >  5:141309/1‑149 (MQ=255)                                                                                                      ccGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTgca                                             <  6:21839/149‑1 (MQ=255)                                                                                                      ccGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTgca                                             <  6:26819/149‑1 (MQ=255)                                                                                                           cGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGcagcag                                         <  6:338051/148‑1 (MQ=255)                                                                                                               aacaTCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACACAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGcagcag                                         >  6:277752/1‑144 (MQ=255)                                                                                                                acaTCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACACAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATc                                   <  5:277752/149‑1 (MQ=255)                                                                                                                   tCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCgag                                <  7:285170/149‑1 (MQ=255)                                                                                                                         tCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAgcgc                          <  8:86115/149‑1 (MQ=255)                                                                                                                           cAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAGCGCaa                        >  2:169539/1‑149 (MQ=255)                                                                                                                                 aTGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAGCGCAAGCAGCt                  <  6:224895/149‑1 (MQ=255)                                                                                                                                    gCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAGCGCAAGCAGCTgg                <  1:167581/148‑1 (MQ=255)                                                                                                                                      cAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAGCGCAAGCAGCTGGaaa             <  5:281270/149‑1 (MQ=255)                                                                                                                                                 tGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCCGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAGCGCAAGCAGCTGGAAAGCCAACTGGTg  >  5:63983/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                   GCTGTTGCAGGTAGTCGTCTGCACTGCCTACTCGGACTATTCCTGGGATGAGTTGCTCGACCGGCTGCAGGCCCACGATCGCTTGCT‑GATCCTGAAAAAACCGTTCGACAACATCGAGGTCCAGCAAATGGCCAGCACCTTGCTGACCAAGTGGGAAATGACCCAACGAGCCTCGCTGAAAATGCACCAGCTCGAACAGCGGGTAGAGCGGCGTACCCAGCAACTGACCCAGGCCAGCGAGGCGCTGCAGCAGGAGATCGAGGAGCGCAAGCAGCTGGAAAGCCAACTGGTG  >  NC_002947/3349824‑3350115

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑