Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,592,156	A→T	7.9%	A117A (GCA→GCT)	PP_2270 →	DNA primase/helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,592,156	0	A	T	7.9%	140.7 / 3.4	51	A117A (GCA→GCT)	PP_2270	DNA primase/helicase
Reads supporting (aligned to +/- strand):  ref base A (27/20);  new base T (2/2);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.69e-01

CAAAGTTGACCCTCTTCGGCCAGAACCTTTGGGCGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGCAAGATCGCCACG  >  NC_002947/2592008‑2592297                                                                                                                                                     |                                                                                                                                              cAAAGTTGACCCTCTTCGGCCAGAACCTTTGGGCGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGgcagca                                                                                                                                               <  4:104410/149‑1 (MQ=255)           ccTCTTCGGCCAGAACCTTTGGGCGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGcc                                                                                                                                      >  8:100725/1‑148 (MQ=255)              ctTCGGCCAGAACCTTTGGGCGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATc                                                                                                                                   >  3:68396/1‑148 (MQ=255)                      aGAACCTTTGGGCGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGaaa                                                                                                                           >  6:286499/1‑148 (MQ=255)                                  cGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCTTGCTGGACGCTATGTCTGTCTCCCAGGTGCAAACAAACAAGTGGCCCGTGGGGTCGCTCCCGAACGGGTCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTg                                                                                                              <  5:252752/149‑1 (MQ=255)                                  cGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTg                                                                                                              <  4:190590/149‑1 (MQ=255)                                                 agaTTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCgaagaa                                                                                               <  7:38406/149‑1 (MQ=255)                                                            aCCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCgaagaa                                                                                               <  1:299313/138‑1 (MQ=255)                                                            aCCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCgaagaa                                                                                               >  2:299313/1‑138 (MQ=255)                                                                     gAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGatat                                                                           <  5:286499/149‑1 (MQ=255)                                                                       gCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATgg                                                                         <  4:68396/149‑1 (MQ=255)                                                                                tATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCgg                                                                >  7:262436/1‑149 (MQ=255)                                                                                tATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAACGCCATCCAGCGAAACATCGAATATCTCGAGATCTTCGAAGAACTCATCCTCATGTTCGATATCGACGAACCga                                                                >  4:19203/1‑148 (MQ=255)                                                                                        tctcCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCcgcg                                                          >  4:51058/1‑147 (MQ=255)                                                                                          tcCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCGGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAagc                                                      >  8:77016/1‑149 (MQ=255)                                                                                            ccAGGTGCAAAACAACAAGTTGCCCGTTGTGTCGATCACGAACGGGGCTTCGTCATCAAGCAAGGGCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCATCATGTTCGATATGGACGAACCGGGCCGCGAagca                                                     <  3:19203/148‑1 (MQ=255)                                                                                            ccAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGaa                                                                                                                    <  5:221943/85‑1 (MQ=255)                                                                                            ccAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGaa                                                                                                                    >  6:221943/1‑85 (MQ=255)                                                                                                   cAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTgg                                                                                                             <  6:57012/85‑1 (MQ=255)                                                                                                   cAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTgg                                                                                                             >  5:57012/1‑85 (MQ=255)                                                                                                       acaacaAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATgc                                         >  8:19148/1‑149 (MQ=255)                                                                                                         aacaaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCGGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATgcgc                                       <  7:77016/149‑1 (MQ=255)                                                                                                         aacaaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATgcg                                        >  7:54827/1‑148 (MQ=255)                                                                                                         aacaaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATgcg                                        >  6:179560/1‑148 (MQ=255)                                                                                                         aacaaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATgcg                                        >  6:222227/1‑148 (MQ=255)                                                                                                         aacaaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACAAACCGGGCCGCGAAGCAGCGCAGGAATgcg                                        >  3:1326/1‑148 (MQ=255)                                                                                                          acaaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCTCGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATgcg                                        >  5:18546/1‑147 (MQ=255)                                                                                                          acaaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCTCGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCa                                      >  5:13983/1‑149 (MQ=255)                                                                                                            aaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCa                                      >  4:43662/1‑147 (MQ=255)                                                                                                            aaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCa                                      >  4:39609/1‑147 (MQ=255)                                                                                                            aaGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGAGATGGCCGATCCGGGCCGCGAAGCAGCGCATGAATTCGCa                                      >  7:48064/1‑147 (MQ=255)                                                                                                              gTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGc                                  >  1:140992/1‑149 (MQ=255)                                                                                                                    cGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCTCGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCa                            <  6:13983/149‑1 (MQ=255)                                                                                                                    cGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCTCGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCa                            <  6:18546/149‑1 (MQ=255)                                                                                                                    cGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGaa                                                        >  3:244346/1‑121 (MQ=255)                                                                                                                    cGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGaa                                                        <  4:244346/121‑1 (MQ=255)                                                                                                                    cGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAag                                                       <  3:68317/122‑1 (MQ=255)                                                                                                                    cGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAag                                                       >  4:68317/1‑122 (MQ=255)                                                                                                                        gtgtCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACAAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGcc                         <  4:1326/148‑1 (MQ=255)                                                                                                                           tCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAgg                     >  1:11785/1‑149 (MQ=255)                                                                                                                            cGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAgg                     >  8:69593/1‑148 (MQ=255)                                                                                                                               tCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAg                 >  7:31951/1‑149 (MQ=255)                                                                                                                                 ccGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTg               >  3:229421/1‑149 (MQ=255)                                                                                                                                 ccGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAAAATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTg               >  7:8566/1‑149 (MQ=255)                                                                                                                                  cGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAATCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCaa                  <  5:165389/145‑1 (MQ=255)                                                                                                                                  cGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAATCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCaa                  >  6:165389/1‑145 (MQ=255)                                                                                                                                  cGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGc              <  7:69593/149‑1 (MQ=255)                                                                                                                                    aaCGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGCaa            <  5:222227/149‑1 (MQ=255)                                                                                                                                        gggCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGCAAGATc        <  2:140992/149‑1 (MQ=255)                                                                                                                                            tCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGCAAGATCGCCa    <  3:51058/149‑1 (MQ=255)                                                                                                                                              cGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGCAAGATCGCCACg  <  3:43662/149‑1 (MQ=255)                                                                                                                                              cGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGCAAGATCGCCACg  <  3:39609/149‑1 (MQ=255)                                                                                                                                                     aCGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGc                                                              <  5:18692/82‑1 (MQ=255)                                                                                                                                                     aCGCAAGGCCATCCAGCGAAACATCGAATATATGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGc                                                              >  6:18692/1‑82 (MQ=255)                                                                                                                                                     |                                                                                                                                              CAAAGTTGACCCTCTTCGGCCAGAACCTTTGGGCGAGTGGGGGCAAGAAGATTGTTGTCACCGAAGGCGAGCTGGACGCTATGTCTGTCTCCCAGGTGCAAAACAACAAGTGGCCCGTGGTGTCGCTCCCGAACGGGGCTCCGGCAGCACGCAAGGCCATCCAGCGAAACATCGAATATCTGGAGAGCTTCGAAGAAGTCATCCTCATGTTCGATATGGACGAACCGGGCCGCGAAGCAGCGCAGGAATGCGCAGAGCTATTCAGCCCAGGCAAGTGCAAGATCGCCACG  >  NC_002947/2592008‑2592297

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: ‑