Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,027,694	C→G	8.7%	A246P (GCC→CCC)	PP_3552 ←	two‑component system sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,027,694	0	C	G	8.7%	137.8 / 3.9	46	A246P (GCC→CCC)	PP_3552	two‑component system sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base C (20/22);  new base G (2/2);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

CTGCTCGCTGATACGCTGCAGGCCCTGGCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAGGTCTCACGGATCGCCCGGCTGGCGATTTCGAACCAA  >  NC_002947/4027548‑4027842                                                                                                                                                      |                                                                                                                                                     cTGCTCGCTGATACGCTGCAGGCCCTGGCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGc                                                                                                                                                      >  4:224090/1‑147 (MQ=255)      cGCTGATACGCTGCAGGCCCTGGCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCtcg                                                                                                                                               <  1:229761‑M2/149‑4 (MQ=255)       gCTGATACGCTGCAGGCCCTGGCTTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCtcgc                                                                                                                                              >  2:83712‑M2/1‑145 (MQ=255)                 tGCAGGCCCTGGCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGc                                                                                                                                    >  7:223029/1‑149 (MQ=255)                   cAGGCCCTGGCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGc                                                                                                                                    >  1:120966/1‑147 (MQ=255)                         cTGGCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCggg                                                                                                                            <  8:84804/149‑1 (MQ=255)                            gCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCAc                                                                                                                         >  2:234699/1‑149 (MQ=255)                                 cccGCTCGTGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGAGCTGGCCTCGGGCA‑cgcccacgagatcaatcag                                                                                                                                <  2:264183‑M2/139‑20 (MQ=255)                                 cccGCTCGTGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGAGCTGGCCTCGGGCA‑cgcccacgagatcaatcag                                                                                                                                >  1:264183‑M2/1‑120 (MQ=255)                                 cccGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTgc                                                                                                                    <  3:224090/149‑1 (MQ=255)                                 cccGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTCACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTgc                                                                                                                    <  1:6471/149‑1 (MQ=255)                                     cTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGAGCTGGCCTCGGGCA‑cgcccacgagatcaatcagccactgg                                                                                                                         >  5:276834‑M2/1‑116 (MQ=255)                                     cTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGAGCTGGCCTCGGGCA‑cgcccacgagatcaatcagccactgg                                                                                                                         <  6:276834‑M2/142‑27 (MQ=255)                                       cgcgcgCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAgg                                                                                                              >  7:171726/1‑149 (MQ=255)                                             ccTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTcc                                                                                                        <  2:69007/149‑1 (MQ=255)                                                 gggATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTgcg                                                                                                    <  2:120966/149‑1 (MQ=255)                                                   gATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAg                                                                                                                                 >  2:142607/1‑118 (MQ=255)                                                   gATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAg                                                                                                                                 <  1:142607/118‑1 (MQ=255)                                                            ccAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATgcg                                                                                          >  4:103172/1‑148 (MQ=255)                                                             cAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATgcgc                                                                                         >  6:342516/1‑148 (MQ=255)                                                                 cccTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGt                                                                                    <  5:342516/149‑1 (MQ=255)                                                                   cTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGa                                                                                  >  6:305617/1‑149 (MQ=255)                                                                   cTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGa                                                                                  >  4:281892/1‑149 (MQ=255)                                                                         gTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTcgc                                                                            <  3:281892/149‑1 (MQ=255)                                                                         gTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTcgc                                                                            <  5:305617/149‑1 (MQ=255)                                                                             cGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGAt                                                                                 >  6:248644/1‑140 (MQ=255)                                                                             cGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGAt                                                                                 <  5:248644/140‑1 (MQ=255)                                                                               cTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGaca                                                                      <  8:223029/149‑1 (MQ=255)                                                                                    tGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCt                                                                  >  8:255522/1‑148 (MQ=255)                                                                                        gTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCCGAAGGTGAGTTCGCGGGACACGCTGacca                                                             >  4:204263/1‑149 (MQ=255)                                                                                           ggCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGaccacc                                                           <  1:234699/148‑1 (MQ=255)                                                                                           ggCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGaccacc                                                           <  7:255522/148‑1 (MQ=255)                                                                                             cATAGTTGACCACCGCGGCCAGTGGCTGATTGATCCTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTc                                                         >  1:221492/1‑149 (MQ=255)                                                                                              aTAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTcca                                                       >  1:323678/1‑149 (MQ=255)                                                                                              aTAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTcca                                                       >  1:130891/1‑149 (MQ=255)                                                                                              aTAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTcca                                                       >  2:232601/1‑149 (MQ=255)                                                                                                    gACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCaccacc                                                  <  6:323548/148‑1 (MQ=255)                                                                                                         ccGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACg                                                                    <  6:347953/125‑1 (MQ=255)                                                                                                         ccGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACg                                                                    >  5:347953/1‑125 (MQ=255)                                                                                                            cgGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGgtg                                         <  2:229761/149‑1 (MQ=255)                                                                                                            cgGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGgtg                                         <  3:103172/149‑1 (MQ=255)                                                                                                               ccAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAg                                      >  7:160762/1‑149 (MQ=255)                                                                                                                                 tcGTGGGCGA‑‑TGCCCGAGGCCAGCtcgcccacgagatcaatcagccactggccgcggtggtcaactatgccaacgccagtcagcgttacctgcagggcctggaacgtgatccccaggcgcgcgagcgggtaggccagggcctgcagcg                      <  6:64795‑M2/148‑125 (MQ=255)                                                                                                                                   gTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAGGTCTCACGGATCGc                        <  2:323678/144‑1 (MQ=255)                                                                                                                                               cccGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAGGTCTCACGGATCGCCAGCCGGGCGAtcc          <  2:130891/148‑3 (MQ=255)                                                                                                                                                  gAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAGGTCTCACGGATCGCCCGGCTGGCGATTTCGaa      >  2:247560/1‑149 (MQ=255)                                                                                                                                                  gAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAGGTCTCACGGATCGCCCGGCTGGCGATTTCGaa      <  1:247560/149‑1 (MQ=255)                                                                                                                                                      ccAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAGGTCTCACGGATCGCCCTCCTGGAGATTTCTAACaaa  >  6:141074/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                     CTGCTCGCTGATACGCTGCAGGCCCTGGCCTACCCGCTCGCGCGCCTGGGGATCACGTTCCAGGCCCTGCAGGTAACGCTGACTGGCGTTGGCATAGTTGACCACCGCGGCCAGTGGCTGATTGAT‑CTCGTGGGCGA‑‑TGCCCGAGGCCAGCTCGCCCAGGGTAGCGAGGCGGGCACTGTGCGCCAGGCTTTCCTGCGCTTCGATGCGCAAGGTGATGTCGCGGGACACGCTGACCACCTCCACCACCGCACCGGTGTAGGTCTCACGGATCGCCCGGCTGGCGATTTCGAACCAA  >  NC_002947/4027548‑4027842

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑