Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,684,016	A→G	11.4%	S379G (AGC→GGC)	rstB →	sensory histidine kinase RstB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,684,016	0	A	G	11.4%	117.2 / 6.3	51	S379G (AGC→GGC)	rstB	sensory histidine kinase RstB
Reads supporting (aligned to +/- strand):  ref base A (20/24);  new base G (2/4);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.38e-01

CCTGCGGTACTGCCATTCAACGGTTGAAACCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATG  >  NC_000913/1683874‑1684152                                                                                                                                                |                                                                                                                                         ccTGCGGTACTGCCATTCAACGGTTGAAACCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATCGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATCTCTTTGAACCTTTTGT‑TCGCCTCGAGCCCa                                                                                                                                          >  1:171669/1‑143 (MQ=255)             ccATTCAACGGTTGAAACCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCCTTGAACCTTTTGT‑ACGCCTCGATCGCCGACGGGATCgtt                                                                                                                              >  2:250126/1‑141 (MQ=255)              gaTTCAACGGTTGAACCCAGCCTGCTACTGTCGGGGAATAGAGCGACATGAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCGGCTGGGATCgagg                                                                                                                             <  1:1101814/142‑4 (MQ=255)              cATTTAGCGGTTGAAACCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATCGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCGGCTGGGATCgagg                                                                                                                             <  2:506318/143‑4 (MQ=255)                 tCATCGGTTGAATCCAGCCTGCTACTGTCGGGGAATAGAGCGACAGTAATAGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCGGCTGGGATCgaggcga                                                                                                                          <  1:531647/143‑7 (MQ=255)                          gAAACCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTGGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTg                                                                                                                 <  2:225730/143‑1 (MQ=255)                           aaaCCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGc                                                                                                                >  1:549904/1‑143 (MQ=255)                            aaCCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCggcggccacg                                                                                                               >  2:366898/1‑139 (MQ=255)                              ccAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGTGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCggg                                                                                                             <  2:280311/143‑1 (MQ=255)                                 gCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCgggctg                                                                                                          >  1:559566/1‑143 (MQ=255)                                    tGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGG‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCgggctgggg                                                                                                       <  1:432253/143‑1 (MQ=255)                                    cgccaCTGTCGGGGAATAGAGCGACATTAATCGTCGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACACATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCgggctgggg                                                                                                       <  1:544181/139‑1 (MQ=255)                                       tACTGTCGGGGAATAGAGCGACATTAATTGGTGAGGATGATGGCCCAGGGATTGCCCCAGAGAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCgggctggggctg                                                                                                    <  1:96044/143‑1 (MQ=255)                                        aCTGTCGGGGAATAGAGCGAAATAAATTTGTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGggctggggctgg                                                                                                   <  2:442737/143‑1 (MQ=255)                                           gTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCaa                                                                                                <  1:111765/143‑1 (MQ=255)                                               gggAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGt                                                                                            <  1:1049370/143‑1 (MQ=255)                                                gaaaTAGGGCGGCGTTAATTGTTGAGGTTGATGCCCCAGGCATTGCCCCAGAAAACCGCGAACATATCTTCGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTc                                                                                           <  1:227078/141‑1 (MQ=255)                                                 gagtAGAGCGACAGTAACTGTGGGGGATGATGGCCCAGGGATTGCCCCAGAAATCCGCGAACATATCTTTGAACCTTTTGT‑TCGCCGCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTcc                                                                                          <  1:586274/140‑1 (MQ=255)                                                      gagCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCActct                                                                                     <  1:1109842/143‑1 (MQ=255)                                                        gCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAAGTGTCCACTCtat                                                                                   >  1:539890/1‑143 (MQ=255)                                                                 atttctcaGGACGATTGCCCAGGGAGTGCCCCAGAAAACCGCTAACCTATCTTTGACCCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGTTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACCGGc                                                                          <  2:987910/136‑1 (MQ=255)                                                                       gAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATggg                                                                    <  1:888409/143‑1 (MQ=255)                                                                       gAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCCCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTGTAGCACTGGCCGTggg                                                                    >  1:854184/1‑143 (MQ=255)                                                                             gatgGTTCAGGGATTGCCCCAGAAAACCGCGAGCAGATCTTTGAACCTGTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTAc                                                              <  1:531420/143‑1 (MQ=255)                                                                             gatgGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTAc                                                              >  1:840889/1‑143 (MQ=255)                                                                              atgGCCCAGGGCTGGCGCCAGAAAACCGCGAACATATCTTTGAACCTTTGTT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACg                                                             <  1:591500/143‑1 (MQ=255)                                                                                ggCCCACGGCTTGCCCGCGAACTCGTCGAACTTAGGTTTGCACCTTGTGTCTCG‑CTCGATCCCGGCCGGGATATCTCAACCGGAGGCTGCGGGCTGTGGTTGGTAATTGTCCATTCCATAGCACTGGCAATGGGCGGTACGGt                                                           <  2:1034010/143‑1 (MQ=255)                                                                                 gCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCCACCGGCGGCTGCGGGCTGGGGCTGGCAAATCTCCACGCTATAGCACTCGCAATGGGCGGTACCGtc                                                          >  1:248053/1‑142 (MQ=255)                                                                                            gCCCCCGGAAACCGCGAAGAGATCTGTGAACCTTTTGT‑GCGCCTCGATCCCAGCGGGGATCGTTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGGAATGGGCGGTACGGTTAATTGTGacac                                               <  2:563149/143‑1 (MQ=255)                                                                                              cccAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCa                                             >  1:116456/1‑143 (MQ=255)                                                                                               ccAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAg                                            <  1:113225/143‑1 (MQ=255)                                                                                                    aaaCCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGGTAGTTGTGACACCAGCGGAc                                       >  1:563285/1‑143 (MQ=255)                                                                                                      aCCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGGTGATTGTGGAGCCAGCGAAccg                                     >  1:698565/1‑141 (MQ=255)                                                                                                        cgcgAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTcgg                                   >  2:107325/1‑143 (MQ=255)                                                                                                          cgAACATATCTTTGAACCTTGTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGggtg                                 <  2:487795/143‑1 (MQ=255)                                                                                                            accATATCTTTGAACCTTTTGT‑CCGCCTCGACCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCAGCACGGTTAATTGTGACACCAGCGAACTGggtggt                               <  1:267298/141‑1 (MQ=255)                                                                                                              cATATCTTTGATCCTTTTGT‑CCGCCTCGATCCCAGCCGGGATCGCTCAGCCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGc                             <  1:1101349/143‑1 (MQ=255)                                                                                                              cATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGc                             >  2:1005445/1‑143 (MQ=255)                                                                                                                tatCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAGTTGTCCACTCTATAGCACTGGCAATGGGCGGTAAGGATAATTGGGAGACCAGCGAACTGGGTGGGGccc                           >  2:66665/1‑143 (MQ=255)                                                                                                                tatCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATCGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGccc                           >  1:109119/1‑143 (MQ=255)                                                                                                                tatCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGccc                           >  1:972497/1‑143 (MQ=255)                                                                                                                    tttGAACCTTTTGT‑TCGCCTCGAGCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCGGGCAATTGTCCTCTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCtt                       <  2:776543/143‑1 (MQ=255)                                                                                                                       gAATCTTTAGT‑TCGCGACGATCCCAGCAGGGATCGGTCAACCGGCGGCGGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTtctc                    <  1:275802/143‑1 (MQ=255)                                                                                                                          ccTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCCATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGGTAATTGTGACACCCGCGAACTGGGTGGCGCCCGCTTCTCGtt                 >  1:393113/1‑143 (MQ=255)                                                                                                                          ccTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGtt                 <  1:1005445/143‑1 (MQ=255)                                                                                                                          ccTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGtt                 >  2:361693/1‑143 (MQ=255)                                                                                                                            ttttGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTa               >  2:586864/1‑143 (MQ=255)                                                                                                                            ttttGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTa               >  1:843491/1‑143 (MQ=255)                                                                                                                            ttttGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTa               <  2:840889/143‑1 (MQ=255)                                                                                                                                      gagcGATCCCGGCTGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGGGACGAGCACACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGt      >  1:515513/4‑143 (MQ=255)                                                                                                                                        gcGATCCCGGCTGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGGTTAGCTGGCCGTTa    >  2:460915/2‑143 (MQ=255)                                                                                                                                          gATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGGTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGGTTAGCGGGCCGtgctc  >  1:94876/1‑139 (MQ=255)                                                                                                                                                |                                                                                                                                         CCTGCGGTACTGCCATTCAACGGTTGAAACCAGCCTGCTACTGTCGGGGAATAGAGCGACATTAATTGTTGAGGATGATGGCCCAGGGATTGCCCCAGAAAACCGCGAACATATCTTTGAACCTTTTGT‑TCGCCTCGATCCCAGCCGGGATCGCTCAACCGGCGGCTGCGGGCTGGGGCTGGCAATTGTCCACTCTATAGCACTGGCAATGGGCGGTACGGTTAATTGTGACACCAGCGAACTGGGTGGTGCCCGCTTCTCGTTTAGCTGGCCGTTATG  >  NC_000913/1683874‑1684152

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑