Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,903,708	C→A	9.5%	intergenic (+233/‑38)	PP_1703 → / → nirB	assimilatory nitrate reductase/sulfite reductase/nitrite reductase large subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,903,708	0	C	A	9.5%	153.2 / 2.5	54	intergenic (+233/‑38)	PP_1703/nirB	assimilatory nitrate reductase/sulfite reductase/nitrite reductase large subunit
Reads supporting (aligned to +/- strand):  ref base C (24/23);  new base A (4/2);  total (29/25)
Fisher's exact test for biased strand distribution p-value = 6.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAGGCAACCCAGGCAACCCACGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGAACAACTGGTCAGTCGCGGCGCCCTGCAGCG  >  NC_002947/1903572‑1903855                                                                                                                                         |                                                                                                                                                      acaGGCAACCCAGGCAACCGACGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGTTACATCAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAAGCGCCTGGAGCCGAAGCTCCAGgc                                                                                                                                             <  1:189834/147‑1 (MQ=255)     gcaacccaggcaacccaCGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑tttt                                                                                                                                      >  5:110907/1‑149 (MQ=255)      caacccaggcaacccaCGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCGCCAGGCGC‑ttttt                                                                                                                                     >  4:261714/1‑149 (MQ=255)            aggcaacccaCGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTAACGTGATGAATACAGGCAAAGGCGCCTGCAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGa                                                                                                                               >  8:223642/1‑149 (MQ=255)              gcaacccaCGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTGGGGTCCAGGCGC‑TTTTTTTTTGATc                                                                                                                             >  6:159356/1‑149 (MQ=255)                aacccaCGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATc                                                                                                                             >  5:202506/1‑147 (MQ=255)                     aCGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATc                                                                                                                      >  8:59816/1‑149 (MQ=255)                        cAACCCGATTGGCACGCTCCCGGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCCATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGc                                                                                                                   <  4:78923/149‑1 (MQ=255)                         aaCCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCt                                                                                                                  >  2:51650/1‑149 (MQ=255)                             cGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTAt                                                                                                               >  1:223136/1‑148 (MQ=255)                              gATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGGGC‑TTTTTTTTTTATCGAGGTTCGGCTTTTg                                                                                                              >  8:212886/1‑148 (MQ=255)                              gATTGGCACGCGCCCTGCTTAACCTCGCATCCAACAAAGCCCACTGATCAACGGCGAGCAACCGGGCCCCCTACCCTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGa                                                                                                             <  6:25825/149‑1 (MQ=255)                                ttGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAg                                                                                                           <  5:236847/149‑1 (MQ=255)                                   gCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGAGCGGCTTATGAAGGc                                                                                                         >  4:54139/1‑148 (MQ=255)                                         tCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGAt                                                                                                                              <  2:92932/121‑1 (MQ=255)                                           cgtGCTTAACCTCGGATACAACAAAGCCCACTGCTCAACGGCGATCAACCGGGCCCCATACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGAGC‑TTTTTTTTTGATCGAGGCTCGGCTTATGAAGGCAACAGCgcg                                                                                                >  6:208316/3‑147 (MQ=255)                                           ccTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGag                                                                                                <  8:88725/149‑1 (MQ=255)                                            cTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGCTTTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGag                                                                                                <  6:110907/149‑1 (MQ=255)                                                  acccTCGGATACAACACACCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCg                                                                                           <  8:243094/145‑1 (MQ=255)                                                   aCCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCggg                                                                                         >  5:145847/1‑148 (MQ=255)                                                         gATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAAc                                                                                     >  5:225736/1‑146 (MQ=255)                                                          aTACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACgaga                                                                                 <  5:26382/149‑1 (MQ=255)                                                          aTACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACga                                                                                   >  7:247531/1‑147 (MQ=255)                                                           aacaacaAAGCCCACTGATCAACGGCGATCAACCGGGCCCCATACCGTGAAGAATACAGGCAAATGCGCCTGGAGCTTCGGCAGCAGGCGC‑TTATTTTTTGAAGGAGCGTCGCCTTATCAAGCCAACAGCGGCCCGCCTGCAACCaga‑g                                                                               >  8:12465/2‑149 (MQ=255)                                                            acaacaAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGCTTTTTTTTTTGATCGAGGATAGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGaga‑g                                                                               >  7:253211/1‑149 (MQ=255)                                                            acaacaAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTAGGCTCCAGGCGC‑TTTTTTTTTTATGGAGGATCGGGTTTTTAAGGGCACAGGGCGCAGCGGGCAACGAgc‑gc                                                                              >  2:131661/1‑149 (MQ=255)                                                             caacaaAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑Gc                                                                              <  7:223642/148‑1 (MQ=255)                                                              aacaaAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGa                                                                            >  7:51557/1‑149 (MQ=255)                                                              aacaaAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGAAACAGCGag                                                                                                >  2:60078/1‑130 (MQ=255)                                                              aacaaAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCGTTTGAAGGCAACAGCGAGCAGCGGGCAACGGCA‑GCg                                                                             >  5:25904/1‑148 (MQ=255)                                                              aacaaAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCGTAGGCTCCAGGCGC‑TTTTTTTTTTATAGAGGATAGGGGTATGAAGGCAACACCGCCCACCTGGCACagaga‑ggcc                                                                            >  6:145606/1‑146 (MQ=255)                                                               acaaAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGAACCAGGCGC‑GTTTTTTTTGATCCAGGATCCGCTTATGTAGGCAACAGCCAGCAGCGGGCCAGGAGA‑ACGAc                                                                           >  7:223347/1‑149 (MQ=255)                                                                 aaaGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTg                                                                         <  8:51557/149‑1 (MQ=255)                                                                      ccACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCAt                                                                    >  3:220633/1‑149 (MQ=255)                                                                            aTCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCgg                                                              <  1:141313/149‑1 (MQ=255)                                                                             tCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCgg                                                              <  6:145847/148‑1 (MQ=255)                                                                                 cGGCGATCAACCGGGCCCCCTACGGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACg                                                         <  2:223136/149‑1 (MQ=255)                                                                                 cGGCGATCAACCGGGCCCCCTACCGTTATGAATACAGGCAAAGGCGCCTGGACCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACg                                                         <  3:261714/149‑1 (MQ=255)                                                                                   gCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGc                                                       <  4:220633/149‑1 (MQ=255)                                                                                           ccGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTAGGCTCCAGGCGC‑TTTTTTTTTTATAGAGGATAGGCTTATGAAGGCAAAACCGAGCAGCGGGCAACGAAA‑CCGACAGGTCATAGTAGGCAAAGGCAAGGTCgg                                               >  4:263775/1‑149 (MQ=255)                                                                                            cGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGc                                              >  3:127677/1‑149 (MQ=255)                                                                                            cGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGc                                              <  7:59816/149‑1 (MQ=255)                                                                                                    cTACCGTGTTGAATACAGCCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTg                                      <  7:12465/149‑1 (MQ=255)                                                                                                       ccGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGATGCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGc                                     <  1:51650/148‑1 (MQ=255)                                                                                                        ggTGAGGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTc                                  <  5:145606/148‑1 (MQ=255)                                                                                                             tcaaTACAGCCAACGGCGCCTGGAGCTTCGGCGCCAGGCGCTTTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGaa                               <  1:125539/146‑1 (MQ=255)                                                                                                               aaTACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGaacaa                            <  4:127677/148‑1 (MQ=255)                                                                                                                    aGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGc                                                             >  5:179360/1‑110 (MQ=255)                                                                                                                    aGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑GTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGc                                                             <  6:179360/110‑1 (MQ=255)                                                                                                                      gCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑ATTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑TCGACTGGTCATCGTCGGCAACCGCATGGTCGGCCACCATTGCGTCGaac                              >  1:2946/1‑139 (MQ=255)                                                                                                                        aaaaGCGCCTGGAGCCGAAGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGAACAACTGGTCa                     >  6:224625/1‑146 (MQ=255)                                                                                                                        aaaaGCGCCTGGAGCCGAAGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGAACAACTGGTCa                     <  5:224625/146‑1 (MQ=255)                                                                                                                                    aGCTTCGGCTACAGGCGC‑TTTTTTTTTGATCGACGATCGTCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGTCCACCATTGCGTCGAACAACTGGTCAGTCGCGGCGCCCTGc      <  5:208316/149‑1 (MQ=255)                                                                                                                                        tCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGAACAACTGGTCAGTCGCGGCGCCCTGCAgcg  >  2:243196/1‑149 (MQ=255)                                                                                                                                         cGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGAACAACTGGTCAGTCGCGGCGCCCTg       <  7:2804/143‑1 (MQ=255)                                                                                                                                         cGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGAACAACTGGTCAGTCGCGGCGCCCTg       >  8:2804/1‑143 (MQ=255)                                                                                                                                         |                                                                                                                                                      ACAGGCAACCCAGGCAACCCACGCAACCCGATTGGCACGCTCCCTGCTTAACCTCGGATACAACAAAGCCCACTGATCAACGGCGATCAACCGGGCCCCCTACCGTGATGAATACAGGCAAAGGCGCCTGGAGCTTCGGCTCCAGGCGC‑TTTTTTTTTGATCGAGGATCGGCTTATGAAGGCAACAGCGAGCAGCGGGCAACGAGA‑GCGACTGGTCATCGTCGGCAACGGCATGGTCGGCCACCATTGCGTCGAACAACTGGTCAGTCGCGGCGCCCTGCAGCG  >  NC_002947/1903572‑1903855

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: ‑