Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,506,934	C→T	12.7%	intergenic (+55/‑62)	petC → / → sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,506,934	0	C	T	12.7%	120.3 / 7.2	48	intergenic (+55/‑62)	petC/sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A
Reads supporting (aligned to +/- strand):  ref base C (23/18);  new base T (3/3);  total (27/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.93e-01

GCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGG  >  NC_002947/1506797‑1507080                                                                                                                                          |                                                                                                                                                    gCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCg                                                                                                                                          >  4:338224/1‑149 (MQ=255)  cACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCgg                                                                                                                                         <  6:116565/149‑1 (MQ=255)  cACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCgg                                                                                                                                         <  5:366089/149‑1 (MQ=255)  cACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCACAAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTGGCAATACTGCTAGGCCACCCCgg                                                                                                                                         <  1:324179/149‑1 (MQ=38)    catATGTGTTGATGTATCTGGATTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGgc                                                                                                                                       <  7:356368/147‑1 (MQ=255)     cTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAg                                                                                                                                                   <  7:181367/136‑1 (MQ=255)     cTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAg                                                                                                                                                   >  8:181367/1‑136 (MQ=255)           gtTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑tttt                                                                                                                               >  6:179981/1‑149 (MQ=255)                    tCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCAt                                                                                                                            <  7:153285/143‑1 (MQ=255)                    tCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCAt                                                                                                                            >  8:153285/1‑143 (MQ=255)                    tCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTaaa                                                                                                                       <  3:215001/148‑1 (MQ=255)                    tCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTaaa                                                                                                                       <  7:296811/148‑1 (MQ=255)                     cTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGt                                                                                                                     >  5:249532/1‑149 (MQ=255)                      tGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGtt                                                                                                                    >  4:186001/1‑149 (MQ=255)                        gCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAg                                                                                                                      <  3:338224/145‑1 (MQ=255)                          tttCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑tttt                                                                                                                               >  5:227260/1‑134 (MQ=255)                          tttCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑tttt                                                                                                                               <  6:227260/134‑1 (MQ=255)                             cttcttcGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACaa                                                                                                              <  3:186001/148‑1 (MQ=255)                                          gCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCAAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCgag                                                                                                 >  3:166946/1‑148 (MQ=255)                                                         cGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGgc                                                                                 <  4:166946/149‑1 (MQ=255)                                                         cGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGgc                                                                                 <  5:179981/149‑1 (MQ=255)                                                                  tGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGcaaccaa                                                                         >  3:81848/1‑148 (MQ=255)                                                                  tGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGcaaccaa                                                                         >  7:126641/1‑148 (MQ=255)                                                                    gAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCGTTTTTAATTTAAATTTG‑ACAAGCATACCGGCGCGGCGCCGCTAAAAGGGCGCCACCAAAAg                                                                      >  1:408387/1‑149 (MQ=25)                                                                    gAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAg                                                                      <  8:126641/149‑1 (MQ=255)                                                                               aCTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCAAAAGCAACCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTATCCTggt                                                           >  1:399920/1‑147 (MQ=255)                                                                                       cGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGcc                                                                                                                                                     <  8:267027/52‑1 (MQ=255)                                                                                       cGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGcc                                                                                                                                                     >  7:267027/1‑52 (MQ=255)                                                                                        gCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGgc                                                                                                                                       <  8:60512/65‑1 (MQ=255)                                                                                        gCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑GTTTGATTTTAAGTTTCACAAGCATCCGTGGGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATc                                                  >  1:211569/1‑149 (MQ=39)                                                                                        gCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACACCGGgc                                                                                                                                       >  7:60512/1‑65 (MQ=255)                                                                                          agtagtTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATccc                                                >  6:166459/1‑149 (MQ=255)                                                                                               tttCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCt                                             >  8:53144/1‑147 (MQ=255)                                                                                                ttCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATT‑CCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGAt                                          >  4:275911/1‑148 (MQ=255)                                                                                                     gttgttGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTTCACAAGCATCCGTGCGAGGAGCCGCTACATTGGCGCAACCAACAGGTTAGCCTGCAATTCCCATCCCGCGGCTCACTa                                     >  8:160469/1‑149 (MQ=39)                                                                                                         ttgAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATtc                                  <  6:249532/148‑1 (MQ=255)                                                                                                                   ccGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTGATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTc                       >  8:347211/1‑149 (MQ=255)                                                                                                                   ccGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTc                       >  5:352546/1‑149 (MQ=255)                                                                                                                        gTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTg                  <  2:408387/149‑1 (MQ=255)                                                                                                                           gCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGtt               >  1:258527/1‑149 (MQ=255)                                                                                                                            ccTGGCAATACTGCTAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTa                                     >  4:44499/1‑126 (MQ=255)                                                                                                                            ccTGGCAATACTGCTAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTa                                     <  3:44499/126‑1 (MQ=255)                                                                                                                             ctggCAATACTGCTAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGTTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCt             >  1:72508/4‑149 (MQ=255)                                                                                                                             cTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGcc                    >  7:356975/1‑142 (MQ=255)                                                                                                                             cTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGcc                    <  8:356975/142‑1 (MQ=255)                                                                                                                                gCAGTATTGCCAGGCCACCCCGGGCGCG‑GTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATTGGCGCAACCAAAAGGTTAGCCTGCTATTACGATACCGCTGATCACTATTGTCATCGGGTTCGCCTGGTTCTGGc          >  5:284126/1‑149 (MQ=255)                                                                                                                                gCAGTATTGCCAGGCCACCCCGGGCGCG‑GTTTCATTTAAAGATGCACAAGAATACGTGAGAGGCGCCGCGACATGGGCGCAACCAACAGGATAGCCTGCTATTCCGATACCGCAGATCCCTATTCACAACGGGTTCGCCTGGGTATGGc          >  2:317717/1‑149 (MQ=255)                                                                                                                                gCAATACTGCTAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTg                                                             >  7:86560/1‑98 (MQ=255)                                                                                                                                gCAATACTGCTAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTg                                                             <  8:86560/98‑1 (MQ=255)                                                                                                                                   gTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCga       <  4:81848/149‑1 (MQ=255)                                                                                                                                         ccAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAgg  <  6:352546/148‑1 (MQ=255)                                                                                                                                          |                                                                                                                                                    GCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGAGAAGG  >  NC_002947/1506797‑1507080

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: ‑