Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,506,930	T→C	11.5%	intergenic (+51/‑66)	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	1,506,930	0	T	C	11.5%	128.6 / 8.3	52	intergenic (+51/‑66)	petC/sspA	ubiquinol‑‑cytochrome c reductase cytochrome c1 subunit/stringent starvation protein A
Reads supporting (aligned to +/- strand):  ref base T (26/20);  new base C (3/3);  total (29/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

AAGCCAGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGA  >  NC_002947/1506783‑1507075                                                                                                                                                    |                                                                                                                                                   aaGCCAGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTAtt                                                                                                                                                   >  6:366089/1‑149 (MQ=255)   gCCAGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGc                                                                                                                                                 >  5:116565/1‑149 (MQ=255)   gCCAGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGc                                                                                                                                                 <  8:224135/149‑1 (MQ=255)               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                                                                                                                       >  8:153285/1‑143 (MQ=255)                                  tCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCAt                                                                                                                       <  7:153285/143‑1 (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                                                                                                                          <  6:227260/134‑1 (MQ=255)                                        tttCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑tttt                                                                                                                          >  5:227260/1‑134 (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                                                                    >  7:126641/1‑148 (MQ=255)                                                                                tGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGcaaccaa                                                                    >  3:81848/1‑148 (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)                                                                                                                                                    |                                                                                                                                                   AAGCCAGCGCATCGGCACCTATGTGTTGCTGTATCTGGCTTTCTTCTTCGTATTCGCCTACTTGCTCAAGCGTGAATACTGGAAGGACGTGCACTGATCACGCAGTAGTTTCTGGTTGTTGAACGCGCCCGGGGTGGCCTAGCAGTATTGCCAGGCCACCCCGGGCGCG‑TTTTCATTTAAAGTTGCACAAGCATCCGTGCGAGGAGCCGCTACATGGGCGCAACCAACAGGTTAGCCTGCTATTCCGATCCCGCTGATCACTATTCTCATCGGGTTCGCCTGGTTCTGGCCGA  >  NC_002947/1506783‑1507075

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: ‑