Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,936,285	C→G	9.3%	A24G (GCC→GGC)	PP_3469 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,936,285	0	C	G	9.3%	154.9 / 5.0	54	A24G (GCC→GGC)	PP_3469	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/24);  new base G (3/2);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.51e-01

CTGTCAAATCTATCAGTCGCCCAAGAGATATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTACCGCAGGCTTA  >  NC_002947/3936145‑3936432                                                                                                                                             |                                                                                                                                                      cTGTCAAATCTATCAGTCGCCCAAGAGATATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTa                                                                                                                                             >  1:27727/1‑149 (MQ=255)    tCAAATCTATCAGTCGCCCAAGAGATATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGCCACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGG‑‑CAGCGCttgtc                                                                                                                                          <  5:194205/149‑5 (MQ=255)               attCGCCAAAGAGATATTTCTCGAACATACTCAATCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGa                                                                                                                                <  8:240844/146‑1 (MQ=255)                    cccAAGAGATATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTc                                                                                                                          >  2:80674/1‑149 (MQ=255)                        agagATATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCgta                                                                                                                      <  2:8972/149‑1 (MQ=255)                        agagATATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCg                                                                                                                        >  1:8972/1‑147 (MQ=255)                          agaTATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCgtag                                                                                                                     >  3:171699/1‑148 (MQ=255)                              atTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCgtagta                                                                                                                   <  3:89735/146‑1 (MQ=255)                              atTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCgtagta                                                                                                                   >  4:89735/1‑146 (MQ=255)                                 tctcGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGc                                                                                                              <  2:266061/148‑1 (MQ=255)                                           aCTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATtgt                                                                                                   <  4:261470/149‑1 (MQ=255)                                                cgCCACAACCTCGGTAGATATCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGaa                                                                                              <  4:167913/148‑1 (MQ=255)                                                 gCCGAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAg                                                                                             >  5:21421/1‑149 (MQ=255)                                                  ccAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGc                                                                                            <  6:103732/149‑1 (MQ=255)                                                         cTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAAt                                                                                        >  2:265135/1‑146 (MQ=255)                                                            ggTAGATCTCTATGACCAGCCCGCTGCATCTAGGACACTTCTACATGAATACGCACTTACACTCGGTGCTGACAAGCGCTGCCTCTGGGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGa                                                                                    <  1:80674/149‑1 (MQ=255)                                                            ggTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGT‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTgg                                                                                                               <  2:227606/120‑1 (MQ=255)                                                                gATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGa                                                                              <  7:13561/149‑1 (MQ=255)                                                                gATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGa                                                                              <  7:157783/149‑1 (MQ=255)                                                                  tctcAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGAc                                                                             >  6:94706/1‑148 (MQ=255)                                                                    tcAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCAc                                                                          >  2:145291/1‑149 (MQ=255)                                                                     cAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACg                                                                         >  5:137676/1‑149 (MQ=255)                                                                      aaTGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGc                                                                        >  3:51816/1‑149 (MQ=255)                                                                        tgtcgaGCCCGCTGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCtt                                                                      <  4:171699/144‑1 (MQ=255)                                                                          aCCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGt                                                                    <  5:94706/149‑1 (MQ=255)                                                                               cccGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAgg                                                                 <  4:68661/147‑1 (MQ=255)                                                                               cccGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAgg                                                                 >  3:68661/1‑147 (MQ=255)                                                                                 cGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGctct                                                             <  6:21421/149‑1 (MQ=255)                                                                                   cagcaTCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGa                                                           <  2:27727/149‑1 (MQ=255)                                                                                      caTCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGctct                                                             <  6:94655/144‑1 (MQ=255)                                                                                      caTCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGctct                                                             >  5:94655/1‑144 (MQ=255)                                                                                       aTCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCATACATCGACCACGCTTGTATGCTCTGACATg                                                       >  8:101741/1‑149 (MQ=255)                                                                                        tCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGaa                                                                                              >  6:66665/1‑109 (MQ=255)                                                                                        tCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGaa                                                                                              <  5:66665/109‑1 (MQ=255)                                                                                            ggACACTTCTATATGCTTACGCACTTACACTCGGTGATGACAAGCGCTGC‑‑CAGCGCTACGTTCTTACGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATgg                                                      <  7:101741/144‑1 (MQ=255)                                                                                                 cTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCAc                                             <  1:265135/149‑1 (MQ=255)                                                                                                             tACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCg                                   >  2:33158/1‑147 (MQ=255)                                                                                                                    ttACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTAc                             <  4:37834/146‑1 (MQ=255)                                                                                                                    ttACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTAc                             >  3:37834/1‑146 (MQ=255)                                                                                                                    ttACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACgg                           >  7:106357/1‑148 (MQ=255)                                                                                                                    ttACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACgg                           >  1:71384/1‑148 (MQ=255)                                                                                                                      acacTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGaa                         <  1:145291/148‑1 (MQ=255)                                                                                                                                 tGACAAGCGCTGC‑‑CATCGATACGTTCTTCATTGACAGCTACGTAGTACTGGCCGAATTATTGTGTGAAGACAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCtt              >  6:4887/1‑148 (MQ=255)                                                                                                                                 aacgtaGCGCTGG‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTa             >  1:65047/6‑149 (MQ=255)                                                                                                                                  acgtaGCGCTGG‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTAc            >  5:42808/5‑149 (MQ=255)                                                                                                                                   aCAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAAcc                                     >  2:230038/1‑123 (MQ=255)                                                                                                                                   aCAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTAcc           >  6:76766/1‑149 (MQ=255)                                                                                                                                   aCAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTAc            <  6:137676/148‑1 (MQ=255)                                                                                                                                    gtaGCGCTGG‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTACCg          >  5:68745/3‑149 (MQ=255)                                                                                                                                     aaGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTgg                                                                                                               <  2:100564/47‑1 (MQ=255)                                                                                                                                     aaGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTgg                                                                                                               >  1:100564/1‑47 (MQ=255)                                                                                                                                     aaGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGCCAGCGACCACGCGTGTAGGCTCTGACATGGCCAGATACCCCATAACCCGCAGTACGGCAAACACCTCCTTCCCGc         >  8:169897/1‑149 (MQ=255)                                                                                                                                          cTGG‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTACCGCAGGCt    <  6:68745/149‑1 (MQ=255)                                                                                                                                            gC‑‑CAGCGCTACGTTCTTCCGTGACAGCGCCGTAGTACTGGCCGACTTATTGTGGGAAGCCAATCAGCCAGAGACCACGCTTGTAGTCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTACCGCAGGCTTa  <  7:169897/149‑1 (MQ=255)                                                                                                                                             |                                                                                                                                                      CTGTCAAATCTATCAGTCGCCCAAGAGATATTTCTCGACCATACTCCAGCCAAAACCTCGGTAGATCTCAATGACCAGCCCGCAGCATCTACGACACTTCTACATGCATACGCACTTACACTCGGTGCTGACAAGCGCTGC‑‑CAGCGCTACGTTCTTCCGTGACAGCTCCGTAGTACTGGCCGAATTATTGTGTGAAGCCAATCAGACAGCGACCACGCTTGTAGGCTCTGACATGGCCAGATCACCCATAACCCGCAGTACGGAAAACACCTCCTTACCGCAGGCTTA  >  NC_002947/3936145‑3936432

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑