Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,332,245	C→G	7.6%	intergenic (+28/‑21)	dksA → / → gluQ	RNA polymerase‑binding transcription factor DksA/glutamyl‑Q tRNA(Asp) synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,332,245	0	C	G	7.6%	155.9 / 2.2	51	intergenic (+28/‑21)	dksA/gluQ	RNA polymerase‑binding transcription factor DksA/glutamyl‑Q tRNA(Asp) synthetase
Reads supporting (aligned to +/- strand):  ref base C (22/24);  new base G (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

CGAGTCGTGCGGCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTCGCCGCCCTCGCCTCCTGGCTCGATGCCCGCGC  >  NC_002947/5332100‑5332384                                                                                                                                                   |                                                                                                                                            cGAGTCGTGCGGCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGcatcat                                                                                                                                           <  7:291086/148‑1 (MQ=255)    gTCGTGCGGCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATgcgc                                                                                                                                       <  5:348452/149‑1 (MQ=255)     tCGTGCGGCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGcc                                                                                                                                      >  4:130286/1‑149 (MQ=255)       gTGCGGCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGcccc                                                                                                                                    <  2:1063/149‑1 (MQ=255)        tGCGGCATCGAGATCGGCCGGCGACGACTGGAAGCCCGCCCTACCGACGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGGCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAAGGGGTGGCATGATGCGCCCCg                                                                                                                                   <  8:201693/149‑1 (MQ=255)         gaggCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGAGTGCAAGGAAATTGCCGAGAAAAAGGAAAAACCGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCAGCATGCGCCCCGt                                                                                                                                  >  5:104381/3‑149 (MQ=255)          cGGCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGtt                                                                                                                                 <  1:229579/149‑1 (MQ=255)                 gagaTCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTta                                                                                                                          >  8:247317/1‑149 (MQ=255)                   gaTCGGCCTGCGCCGGCTGGAAGCCCTCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTtata                                                                                                                        <  5:209632/149‑1 (MQ=255)                        gCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGcc                                                                                                                    >  1:7192/1‑148 (MQ=255)                         ccTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCa                                                                                                                  <  7:247317/149‑1 (MQ=255)                           tGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGcatcat                                                                                                                                           <  6:114249/122‑1 (MQ=255)                           tGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGcatcat                                                                                                                                           >  5:114249/1‑122 (MQ=255)                                cgccTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGATCGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGAc                                                                                                           <  1:255103/149‑1 (MQ=255)                                     ggAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGa                                                                                                      >  4:105136/1‑149 (MQ=255)                                           ccgaccTACATCCGACCTGTTCTTCGACTGCAAGGAAATTTCCGAGAAAAATGAAAAATCGGTGGGCATAGGCTGATCTTTCTTCCT‑GCTGAACGGGGCGCATCATTCGAACCGTTTGATTTATATGACAATACTGACCATTACCGAc                                                                                                 <  4:49830/148‑1 (MQ=255)                                                cTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGc                                                                                           <  3:105136/149‑1 (MQ=255)                                                    cgccgACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTAc                                                                                        >  4:305043/1‑148 (MQ=255)                                                    cgccgACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACa                                                                                       >  1:269041/1‑149 (MQ=255)                                                               gCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGAc                                                                                                     <  7:56370/124‑1 (MQ=255)                                                               gCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGAc                                                                                                     >  8:56370/1‑124 (MQ=255)                                                                cTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCg                                                                           <  1:9384/149‑1 (MQ=255)                                                                   cGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCgg                                                                                   >  6:126109/1‑138 (MQ=255)                                                                   cGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCgg                                                                                   <  5:126109/138‑1 (MQ=255)                                                                   cGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGccc                                                                        >  3:34030/1‑149 (MQ=255)                                                                    gACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGcccc                                                                       <  2:269041/149‑1 (MQ=255)                                                                        gCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCAGGCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGcccccac                                                                    >  1:103138/1‑149 (MQ=255)                                                                           aGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGcccccacccc                                                                 >  1:40409/1‑148 (MQ=255)                                                                               aaTTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCg                                                            <  4:34030/149‑1 (MQ=255)                                                                                     cGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCg                                                                           >  4:136479/1‑128 (MQ=255)                                                                                     cGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCg                                                                           <  3:136479/128‑1 (MQ=255)                                                                                     cGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTcc                                                      >  4:116019/1‑149 (MQ=255)                                                                                      gagaAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCGTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCt                                                     >  4:234422/1‑149 (MQ=255)                                                                                        gaAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGc                                                   <  2:40409/149‑1 (MQ=255)                                                                                          aaaaGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCAc                                                 <  3:116019/149‑1 (MQ=255)                                                                                                aaaaaaCGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGc                                           <  7:112942/149‑1 (MQ=255)                                                                                                       ggTCTGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACAt                                                                                      <  2:3409/99‑1 (MQ=255)                                                                                                       ggTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACAt                                                                                      >  1:3409/1‑99 (MQ=255)                                                                                                            gCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTc                                  <  6:72450/146‑1 (MQ=255)                                                                                                            gCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTc                                  >  5:72450/1‑146 (MQ=255)                                                                                                                  gCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTc                                              >  3:81708/1‑128 (MQ=255)                                                                                                                  gCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTc                                              <  4:81708/128‑1 (MQ=255)                                                                                                                    tGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTc                                                       >  2:350793/1‑117 (MQ=255)                                                                                                                    tGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTc                                                       <  1:350793/117‑1 (MQ=255)                                                                                                                     gATCTTTCTTCCA‑CCTGAACGGGGCGCCTCATGCGCCCCGTTTAATTTATATGCCCAGCCGGACCATGACCGCCTCCACCTACAAAGGGCGCTTGGCCCCCACCCCCCCCGGCTACCTGCCATACGGCACGCGGGTCGCCGcccacccc                      >  2:361546/1‑144 (MQ=255)                                                                                                                           tcttcCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTCGCCGCCCTCGcctc                    <  2:7192/145‑1 (MQ=255)                                                                                                                           tcttcCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTCGCCGCCCTCGCCTCCTg                 <  1:71766/148‑1 (MQ=255)                                                                                                                               ccA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTCGCCGCCCTCGCCTCCTGGc               <  3:130286/146‑1 (MQ=255)                                                                                                                               ccA‑CCTGAACGGGGCGCATAATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCCCCCCCACCGGCATCCTGCACTTAGGCTCGCTGGTCGCCGCCCTAGCCTCCAGGCTc             >  6:52451/1‑148 (MQ=255)                                                                                                                                 a‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTCGCCGCCCTCGCCTCCTGGCTCGAt          >  5:35344/1‑149 (MQ=255)                                                                                                                                          ggggCGCATGATGCGCCACGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGCATCGCTCTTCGCCGCCCACGCATCCTGGCTCGATGACCgcgc  >  8:165553/1‑149 (MQ=255)                                                                                                                                          ggggCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTCGCCGCCCTCGCCTCCTGGCTCGATGCCCgcgc  >  6:25132/1‑149 (MQ=255)                                                                                                                                           gggCGCATGATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTg                                     >  7:198132/1‑113 (MQ=255)                                                                                                                                           gggCGCATGATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTg                                     <  8:198132/113‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                            CGAGTCGTGCGGCATCGAGATCGGCCTGCGCCGCCTGGAAGCCCGCCCTACCGCCGACCTGTGCTTCGACTGCAAGGAAATTGCCGAGAAAAAGGAAAAAACGGTCGGCAAAGGCTGATCTTTCTTCCA‑CCTGAACGGGGCGCATCATGCGCCCCGTTTCATTTATATGCCCAGCCTGACCATGACCGACTCCAGCTACATCGGGCGCTTCGCCCCCACCCCCAGCGGCTTCCTGCACTTCGGCTCGCTGGTCGCCGCCCTCGCCTCCTGGCTCGATGCCCGCGC  >  NC_002947/5332100‑5332384

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑