Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,721,305	G→A	7.4%	intergenic (‑267/‑175)	PP_2381 ← / → PP_2382	hypothetical protein/putative transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,721,305	0	G	A	7.4%	150.5 / 2.1	54	intergenic (‑267/‑175)	PP_2381/PP_2382	hypothetical protein/putative transporter
Reads supporting (aligned to +/- strand):  ref base G (22/27);  new base A (2/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.69e-01

TGTTTAAAGTTGATGCTCGTGCCGTGCAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGA  >  NC_002947/2721159‑2721453                                                                                                                                                    |                                                                                                                                                     tgtTTATAGTTGATGCTCGTGCGGTGCATGGGTTTCAGGGCTTGATTTCTGAACGTGACCTGTTGAAGTGCTCTTCTGCACTGTCGTGAAAATGCCGTCGTTTCTGCATTCAATGAATGGTTTTTGTAGGATTATTCCGTG‑TTTCTGAt                                                                                                                                                    <  4:106541/149‑1 (MQ=255)       aaGTTGATGCTCGTGCCGTGCAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAAAGGTTGTTGTAGGAAAATTACTGG‑TTTATTATTTTCGc                                                                                                                                              >  4:220712/1‑149 (MQ=255)          ttGATGCTCGTGCCGTGCAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTg                                                                                                                                           <  6:144645/149‑1 (MQ=255)          ttGATGCTCGTGCCGTGCAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGGGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGGGGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCttt                                                                                                                                           <  6:286572/149‑2 (MQ=255)            gATGCTCGTGCCGTGCAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGc                                                                                                                                          <  8:292685/148‑1 (MQ=255)            gATGCTCGTGCCGTGCAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCGGATTTTCGCTTg                                                                                                                                           >  3:347310/1‑147 (MQ=255)                           cAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTTGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCgt                                                                                                                           <  5:149751/148‑1 (MQ=255)                           cAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCgtt                                                                                                                          <  7:104428/149‑1 (MQ=255)                              gggATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTAATTTTCGCTTGCAGAAAg                                                                                                                                    <  1:281436/136‑1 (MQ=255)                              gggATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTAATTTTCGCTTGCAGAAAg                                                                                                                                    >  2:281436/1‑136 (MQ=255)                                   tCATGGCTCGTTTTCTTTACGTTAGCTGTTGAAGTGCTCTACTGAACAGTCGTTAAAATGCCGTCGGGTCTGCATTGAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACaa                                                                                                                   <  3:220712/148‑1 (MQ=255)                                     aGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACtt                                                                                                                >  3:19006/1‑149 (MQ=255)                                     aGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGGAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACtt                                                                                                                >  2:77435/1‑149 (MQ=255)                                     aGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTCTTGTAGGAAAATTCCGGG‑TTTCTAATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACtt                                                                                                                >  7:180097/1‑149 (MQ=255)                                         atCGAGTTCTGATCGTGATCTGTTGATGTGCTGAAGTGCACTGTCGGGAAAATGCCGTCGGGGCTGGATTCAATGAATGGTTGTTGTAGGAATTTTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCTTCGGCGTTGTTACTACtttgtt                                                                                                            <  4:338298/148‑4 (MQ=255)                                                  tGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTg                                                                                                                                           >  1:173669/1‑109 (MQ=255)                                                  tGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTg                                                                                                                                           <  2:173669/109‑1 (MQ=255)                                                            cTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGcc                                                                                         >  5:221956/1‑149 (MQ=255)                                                                  aaGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCgttgtt                                                                                                                       <  8:11550/113‑1 (MQ=255)                                                                  aaGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCgttgtt                                                                                                                       >  7:11550/1‑113 (MQ=255)                                                                  aaGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGc                                                                                          <  8:13604/142‑1 (MQ=255)                                                                  aaGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGc                                                                                          >  7:13604/1‑142 (MQ=255)                                                                    gTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCt                                                                                   >  8:44098/1‑147 (MQ=255)                                                                      gCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGaaa                                                                                                                                     <  8:266611/95‑1 (MQ=255)                                                                      gCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGaaa                                                                                                                                     >  7:266611/1‑95 (MQ=255)                                                                         cAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTGATGTTGAGCTCAATCCTGGCCGAGTCTTAGAtt                                                                             >  2:193396/1‑148 (MQ=255)                                                                           aCTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAg                                                                          >  2:31075/1‑149 (MQ=255)                                                                               cacaGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTgg                                                                      >  4:188290/1‑149 (MQ=255)                                                                               cacaGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTgg                                                                      <  8:244251/149‑1 (MQ=255)                                                                                      gggAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGc                                                                     <  8:212564/143‑1 (MQ=255)                                                                                      gggAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGc                                                                     >  7:212564/1‑143 (MQ=255)                                                                                        gAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGCAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATAttt                                                             <  1:77435/149‑1 (MQ=255)                                                                                          atatcccGGCGGGTCTGCATTCAAAGAATGGTGGTTGTAGGAAATATCCTGG‑TCTCTGATTAACGCCTGCAGATAGCATCGGCGTTGTTACAACTTTCATGTTCAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTgg                                                           <  8:253910/144‑1 (MQ=255)                                                                                             tGCGGTCGGGTCTGCAATCAAAGAATGGTTGTTGTACGAAAATTCCGGG‑GTTCTGATTTTCGCGGGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCaa                                                        <  6:64421/149‑1 (MQ=255)                                                                                                cGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTg                                                                                                                                           <  3:53548/63‑1 (MQ=255)                                                                                                cGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTg                                                                                                                                           >  4:53548/1‑63 (MQ=255)                                                                                                    gggTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAAt                                                 >  6:308972/1‑149 (MQ=255)                                                                                                    gggTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAAt                                                 <  7:44098/149‑1 (MQ=255)                                                                                                    gggTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTAATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCaa                                                  <  8:180097/148‑1 (MQ=255)                                                                                                      gTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCg                                               >  3:277438/1‑149 (MQ=255)                                                                                                        cTGCATTCAAAGAATGGTTTTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGATTGCCAAATATTGGCCAACTCAATctaa                                             <  6:276448/149‑4 (MQ=38)                                                                                                           cATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGc                                             <  6:221956/146‑1 (MQ=255)                                                                                                            aTTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCa                                          >  3:32460/1‑148 (MQ=255)                                                                                                                aaaGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGATCTCAATCATGGACTAGTCTTAGATTGATTTGGCCAATATTTGGAAATCTCAATCGGCTCAAAgaa                                     >  7:305216/1‑147 (MQ=255)                                                                                                                aaaGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAg                                       >  6:354347/1‑147 (MQ=255)                                                                                                                 aaGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAg                                    <  3:188290/149‑1 (MQ=255)                                                                                                                    aaTGGTTGTTGTAGGAAAATTCCGGGATTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTg                                  >  1:3214/1‑149 (MQ=255)                                                                                                                         ttgttgTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCata                            <  1:31075/149‑1 (MQ=255)                                                                                                                           cttggAGTAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTTTTACAACGTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCatat                           <  2:56084/147‑1 (MQ=255)                                                                                                                                aGGAAAATTCCGGG‑TTTCTGATTTTCGCTGGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCt                     >  3:112106/1‑149 (MQ=255)                                                                                                                                 ggAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATTTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCt                     <  4:19006/148‑1 (MQ=255)                                                                                                                                 ggAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCt                     <  4:277438/148‑1 (MQ=255)                                                                                                                                  gAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTg                    <  5:354347/148‑1 (MQ=255)                                                                                                                                          cGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAg           >  6:163322/1‑149 (MQ=255)                                                                                                                                                    gATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTGAATCCTGGCCGAGTCTTAGATTGAGTTGGGCAATATTTGGGAATCTCAATCGGCTCAAAGGAGTGGCCATTTGAATGTGCAATCCACGTGTTCAggc  >  8:153500/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                                     TGTTTAAAGTTGATGCTCGTGCCGTGCAAGGGATTCAGGGCTCGATTTCTGAACGTGACCTGTTGAAGTGCTCAACTGCACAGTCGGGAAAATGCCGTCGGGTCTGCATTCAAAGAATGGTTGTTGTAGGAAAATTCCGGG‑TTTCTGATTTTCGCTTGCAGAAAGCATCGGCGTTGTTACAACTTTCATGTTGAGCTCAATCCTGGCCGAGTCTTAGATTGAGTTGGCCAATATTTGGCAATCTCAATCGGCTCAAAGGAGTGCCCATATGAATCTGCAATCCAAGTGTTCAGGA  >  NC_002947/2721159‑2721453

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: ‑