Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,691,796	C→G	12.0%	intergenic (+63/‑108)	PP_1487 → / → PP_1488	hypothetical protein/methyl‑accepting chemotaxis transducer

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,691,796	0	C	G	12.0%	141.8 / 9.7	50	intergenic (+63/‑108)	PP_1487/PP_1488	hypothetical protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand):  ref base C (20/24);  new base G (4/2);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 4.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.76e-01

CGAGCTGGCCCGCCAGCTGCGGCTGGACCCGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTGAAGAACTGGACCTTGCGCCAACGGATCCTGG  >  NC_002947/1691655‑1691937                                                                                                                                              |                                                                                                                                                cGAGCTGGCCCGCCAGCTGCGGCTGGACCCGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTcac                                                                                                                                          <  2:85747/149‑1 (MQ=255)          ccGCCAGCTGCGGCTGGACCCGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCaa                                                                                                                                  >  7:44559/1‑148 (MQ=255)              gcccctcGGCTGGACCCGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTc                                                                                                                             <  1:118434/143‑1 (MQ=255)                gCTGCGGCTGGACCCGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCt                                                                                                                           >  7:5484/1‑149 (MQ=255)                   gCGGCTGGACCCGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTg‑‑ac                                                                                                                      >  2:9725/1‑149 (MQ=255)                             ccGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATcaca                                                                                                            >  8:265007/1‑149 (MQ=255)                              cGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACAt                                                                                                           <  3:94188/149‑1 (MQ=255)                               gggCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGACGGAGCGCCGCACGGGCGGCGCTCGATCTCACAGgcgct                                                                                                                                   <  1:299273/126‑2 (MQ=25)                               gggCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGACGGAGCGCCGCACGGGCGGCGCTCGATCTCACAGgcgct                                                                                                                                   >  2:299273/1‑125 (MQ=25)                                       gcCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCg                                                                                                   >  7:262697/1‑148 (MQ=255)                                       gcCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGt                                                                                                  <  2:310497/149‑1 (MQ=255)                                       gcCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGt                                                                                                  <  6:158540/149‑1 (MQ=255)                                         cAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTCAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTaa                                                                                                >  3:254778/1‑149 (MQ=255)                                                  gAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTg‑‑a                                                                                                                       >  3:100863/1‑117 (MQ=255)                                                  gAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTg‑‑a                                                                                                                       <  4:100863/117‑1 (MQ=255)                                                  gAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTgg                                                                                       >  8:20639/1‑149 (MQ=255)                                                  gAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTgg                                                                                       <  8:262697/149‑1 (MQ=255)                                                       ccAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCta                                                                                   >  4:43556/1‑148 (MQ=255)                                                                 ttGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGa                                                                        <  3:43556/149‑1 (MQ=255)                                                                 ttGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGa                                                                        >  2:47722/1‑149 (MQ=255)                                                                      tGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGAtttt                                                                    >  6:336729/1‑148 (MQ=255)                                                                       gCAGCGTAGTGGCGGTGGTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTc                                                                  >  6:16773/1‑149 (MQ=255)                                                                        cAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTcc                                                                 <  1:47722/149‑1 (MQ=255)                                                                          gCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCg                                                                            >  6:215339/1‑136 (MQ=255)                                                                          gCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCg                                                                            <  5:215339/136‑1 (MQ=255)                                                                           cGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGc                                                              <  3:240729/149‑1 (MQ=255)                                                                             tAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTc                                                            <  8:44559/149‑1 (MQ=255)                                                                             tAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTc                                                            <  5:16773/149‑1 (MQ=255)                                                                                tGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTg‑‑acg                                                                                                                     >  3:6734/1‑89 (MQ=255)                                                                                tGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTg‑‑acg                                                                                                                     <  4:6734/89‑1 (MQ=255)                                                                                 ggCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGtt                                                         <  3:202552/148‑1 (MQ=255)                                                                                    ggggCTTGCGACTGCCTATTTAGCGCCTGTGAGATCGAGCGCCGCGCGTGCGGCGCTCCGTCTCACAGTCGCTAAATTCCTGTCTCGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTtgt                                                       <  1:98963/146‑1 (MQ=37)                                                                                       gCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAAtt                                                  >  7:16898/1‑149 (MQ=255)                                                                                         ttGCCACGGCCTATTGAGCGCCTGTGGGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGc                                                              >  8:123738/1‑135 (MQ=255)                                                                                         ttGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGc                                                              <  7:123738/135‑1 (MQ=255)                                                                                         ttGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGAGTTTTCCCGCTCGTTGTGAATTcc                                                >  5:164204/1‑149 (MQ=255)                                                                                           gCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTcc                                                <  3:238253/147‑1 (MQ=255)                                                                                                ggCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGc                                         <  7:265007/149‑1 (MQ=255)                                                                                                        gAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAAtgt                                  >  8:57104/1‑148 (MQ=255)                                                                                                           cgcCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCAAAGGCGCAAGATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTgaa                               <  7:260262/148‑1 (MQ=255)                                                                                                            gcCTGTGAGCTCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTgaag                              >  7:249597/1‑148 (MQ=255)                                                                                                            gcCTGTGAGACGGAGCGCCGCACGGGCGGCGCTCGATCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTgaag                              >  7:6792/1‑148 (MQ=38)                                                                                                              cTGTGAGACGGAGCGCCGCACGGGCGGCGCTCGATCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTga                                <  4:300116/144‑1 (MQ=38)                                                                                                              cTGTGAGACGGAGCGCCGCACGGGCGGCGCTCGATCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTga                                >  3:300116/1‑144 (MQ=38)                                                                                                              cTGTGAGACGGAGCGCCGCACGGGCGGCGCTCGATCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTGAAGAAc                           >  1:328348/1‑149 (MQ=38)                                                                                                                 tgAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGaa                                     <  2:181481/136‑1 (MQ=255)                                                                                                                 tgAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTGAAGAACt                          <  8:16898/147‑1 (MQ=255)                                                                                                                 tgAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTGAAGAACTg                         <  1:9725/148‑1 (MQ=255)                                                                                                                        gAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTGAAGAACTGGACCTTgc                 <  7:20639/149‑1 (MQ=255)                                                                                                                                        gcgcTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTGAAGAACTGGACCTTGCGCCAACGGATCCTgg  >  6:222728/1‑148 (MQ=255)                                                                                                                                              |                                                                                                                                                CGAGCTGGCCCGCCAGCTGCGGCTGGACCCGGGCTTGCGCCAGGAACTGGAAAGCCAGGTGCGGTTGGCTGCAGCGTAGTGGCGGTGCTTGCCACGGCCTATTGAGCGCCTGTGAGATCGAGCGCCGCCCGTGCGGCGCTCCGTCTCACAGGCGCAAAATTCCTG‑‑ACGACAATCACATCAATACCGTAAGACCTCTGGGCTATACTTCGGCGATTTTTCCCGCTCGTTGTGAATTCCTGAGGGCTGAATGTGAAGAACTGGACCTTGCGCCAACGGATCCTGG  >  NC_002947/1691655‑1691937

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: ‑