Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,385,520	Δ1 bp	10.5%	coding (401/576 nt)	PP_2093 ←	two‑component system response regulator NasT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,385,520	0	T	.	10.5%	170.7 / 14.9	57	coding (401/576 nt)	PP_2093	two‑component system response regulator NasT
Reads supporting (aligned to +/- strand):  ref base T (27/24);  new base . (3/3);  total (30/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.07e-01

TGATCTGTTCGGCAACCTGGATCAGCTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCCCTGCCTGGATCGCCTGGCGCATCAT  >  NC_002947/2385371‑2385662                                                                                                                                                      |                                                                                                                                                tGATCTGTTCGGCAACCTGGATCAGCTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAATCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGt                                                                                                                                                 >  2:672286/1‑150 (MQ=255)      tGTTCGGCAACCTGGATCAGCTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTcgcgc                                                                                                                                            <  1:850170/150‑1 (MQ=255)            gCAACCTGGATCAGCTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑Ccagc                                                                                                                                     >  2:61827/1‑150 (MQ=255)                  tGGATCAGCTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGG‑CGCGCGACcagcaattgg                                                                                                                               <  2:803533/150‑6 (MQ=255)                          cTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAg                                                                                                                       <  2:136876/150‑1 (MQ=255)                          cTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAg                                                                                                                       >  1:988088/1‑150 (MQ=255)                           ttCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGACTGCTCGATCCGCTTGCGTTCGGCCACTTGCAGGTCGGGCG‑CCAGCAGCTGTGCCTTCAGt                                                                                                                      <  1:32231/150‑1 (MQ=255)                                   ccGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTc                                                                                                              <  1:547345/150‑1 (MQ=255)                                        tCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCttt                                                                                                         >  2:470686/1‑150 (MQ=255)                                             gCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCttt                                                                                                         >  2:484620/1‑145 (MQ=255)                                             gCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCttt                                                                                                         <  1:484620/145‑1 (MQ=255)                                             gCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAg                                                                                                    >  2:1252862/1‑150 (MQ=255)                                             gCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTACATTTTCCTCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCGGCATCTGTGCCTTCATTGCCTGGTCTCTTTCGAAg                                                                                                    >  2:277543/1‑150 (MQ=255)                                               cTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCg                                                                                                  <  1:102537/150‑1 (MQ=255)                                                    gACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCa                                                                                             >  1:415873/1‑150 (MQ=255)                                                        cATCAGGGTGTAGGCCTGCTCTTCGTTGAAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGc                                                                                         <  2:808347/150‑1 (MQ=255)                                                                tgtAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCa                                                                                 <  2:371777/150‑1 (MQ=255)                                                                     gCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATc                                                                            <  2:762331/150‑1 (MQ=255)                                                                       cTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCgg                                                                          >  1:380455/1‑150 (MQ=255)                                                                       cTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCgg                                                                          >  1:286248/1‑150 (MQ=255)                                                                         gCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCgg                                                                                                 >  2:241422/1‑125 (MQ=255)                                                                         gCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCgg                                                                                                 <  1:241422/125‑1 (MQ=255)                                                                             ttCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCt                                                                                                                  <  1:33682/104‑1 (MQ=255)                                                                             ttCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCt                                                                                                                  >  2:33682/1‑104 (MQ=255)                                                                             ttCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAg                                                                    >  1:1306853/1‑150 (MQ=255)                                                                                 ttGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCtgt                                                                                                                               <  2:282660/87‑1 (MQ=255)                                                                                 ttGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCtgt                                                                                                                               >  1:282660/1‑87 (MQ=255)                                                                                     aGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCgcag                                                            >  2:560464/1‑150 (MQ=255)                                                                                       tCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGG‑CGCGCGACcagcaatt                                                                                                                                 <  1:143666/79‑4 (MQ=38)                                                                                       tCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGG‑CGCGCGACcagcaatt                                                                                                                                 >  2:143666/1‑76 (MQ=38)                                                                                        ccTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGCTCGGCTGCAGCCGCGCAGCAt                                                         <  2:380455/150‑1 (MQ=255)                                                                                          ttCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATgg                                                       >  1:1308503/1‑150 (MQ=255)                                                                                          ttCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATgg                                                       <  1:61827/150‑1 (MQ=255)                                                                                                   atcaGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTcg                                              >  2:674756/1‑150 (MQ=255)                                                                                                    tcaGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTcga                                             <  2:286248/150‑1 (MQ=255)                                                                                                    tcaGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTcga                                             >  2:1331162/1‑150 (MQ=255)                                                                                                    tcaGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTcga                                             >  2:565784/1‑150 (MQ=255)                                                                                                     caGCAAGCCATTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCtt                                                <  2:913280/146‑1 (MQ=255)                                                                                                     caGCAAGCCATTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCtt                                                >  1:913280/1‑146 (MQ=255)                                                                                                       gCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCgg                                                                                                 <  1:1006707/95‑1 (MQ=255)                                                                                                       gCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCgg                                                                                                 >  2:1006707/1‑95 (MQ=255)                                                                                                              cTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCt                                                                                                                                 >  2:835826/1‑56 (MQ=255)                                                                                                              cTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCt                                                                                                                                 <  1:835826/56‑1 (MQ=255)                                                                                                                   ccTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGa                              >  1:464000/1‑150 (MQ=255)                                                                                                                        tCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCcct                         <  1:565784/150‑1 (MQ=255)                                                                                                                            tGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCcctgcct                     <  1:1331162/150‑1 (MQ=255)                                                                                                                                 ttGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCcct                         <  1:888139/141‑1 (MQ=255)                                                                                                                                 ttGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCcct                         >  2:888139/1‑141 (MQ=255)                                                                                                                                     gTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCCCTGCCTGGATCGCCt            >  2:602972/1‑150 (MQ=255)                                                                                                                                     gTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCCCTGCCTGGATCGCCt            >  1:129899/1‑150 (MQ=255)                                                                                                                                        cGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCCCTGCCTGGATCGCCTGgc         <  2:129899/150‑1 (MQ=255)                                                                                                                                         ggCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAg                                     >  1:105474/1‑121 (MQ=255)                                                                                                                                         ggCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAg                                     <  2:105474/121‑1 (MQ=255)                                                                                                                                          gCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTc                                                                                                              <  1:725957/47‑1 (MQ=255)                                                                                                                                          gCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTc                                                                                                              >  2:725957/1‑47 (MQ=255)                                                                                                                                              gctGCTGG‑CGCGCGACCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAGGCGGGCCATGGCCACGTCCAGGATCGGc                                                                         <  1:790577/78‑1 (MQ=255)                                                                                                                                              gctGCTGG‑CGCGCGACCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAGGCGGGCCATGGCCACGTCCAGGATCGGc                                                                         >  2:790577/3‑80 (MQ=255)                                                                                                                                               ctGCTGG‑CGCGCGACCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCCCTGCCTGGATCGCCTGGCGcatcat  >  1:579042/2‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                TGATCTGTTCGGCAACCTGGATCAGCTTCTGCTGCCGGCTCATGGCCTGGCGACGCATCAGGGTGTAGGCCTGCTCTTCGTTGCAGTCCTTCATTTTCATCAGCAAGCCCTTGGCCTGCTCGATGCGCTTGCGTTCGGCCAATTGCTGGTCGCGCG‑CCAGCAGCTGTGCCTTCAGTGCCTGGTCGCTTTCGAAGCGGGCCATGGCCACGTCCAGGATCGGCTGCAGCCGCGCAGCATGGATACCTTCGACGATATAGGCACTGACCCCTGCCTGGATCGCCTGGCGCATCAT  >  NC_002947/2385371‑2385662

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑