Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,005,000	G→C	16.7%	intergenic (+38/‑138)	PP_5259 → / → ydcJ	LysR family transcriptional regulator/metalloprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,005,000	0	G	C	16.7%	119.3 / 16.9	48	intergenic (+38/‑138)	PP_5259/ydcJ	LysR family transcriptional regulator/metalloprotein
Reads supporting (aligned to +/- strand):  ref base G (18/22);  new base C (3/5);  total (21/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.65e-01

CATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGCCCGCC  >  NC_002947/6004852‑6005146                                                                                                                                                     |                                                                                                                                                     cATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACcg                                                                                                                                                      >  6:165044/1‑149 (MQ=255) cATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCCGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTAGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACcg                                                                                                                                                      >  1:29320/1‑149 (MQ=255)     cAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTa                                                                                                                                                  <  5:105077/149‑1 (MQ=255)          cgcAGTGGCGGTGCGGATTACCTGGCGTATGCCGTGGATGGGGCAGAGGTGCCAATGGTGCGTGCGCTGGTGGAATGGATTGGCGAGGAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGgcgc                                                                                                                                             <  2:88086/149‑1 (MQ=255)               tGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGTGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCtt                                                                                                                                        <  8:3829/149‑1 (MQ=38)                 ccGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCtt                                                                                                                                        >  8:265570/1‑147 (MQ=255)                      gcgcATTACCTGGCGTATGCCGAGCCTGCGGCAGAGGTGCCAACGGTGCGGGCGCTGGTGGAATGGATTGGCTAGCAGTTGCAGGGTTGACGGCCTCTTCGCGGCTAACGCCGCTCCTCCGGTGACCGCGTAGGCGCGGCTTTAGCCgg                                                                                                                                 <  1:75527/149‑1 (MQ=255)                      gcgcATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCCTTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCgc                                                                                                                                 <  3:197700/149‑2 (MQ=25)                         cATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGa                                                                                                                               >  5:315157/1‑148 (MQ=255)                             aCCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑g‑g                                                                                                                         <  2:277017/148‑1 (MQ=255)                               cTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGCGaa                                                                                                                              >  8:245175/1‑143 (MQ=25)                               cTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGCGaa                                                                                                                              <  7:245175/143‑1 (MQ=25)                               cTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGGTGCAGGTTTGCCGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGGAGGCGGGGCGTTAGGCGGGAAC‑G‑GGcc                                                                                                                      >  8:209357/1‑149 (MQ=39)                                  gCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTc                                                                                                                   >  5:121852/1‑149 (MQ=255)                                            aGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATc                                                                                                         <  4:74850/149‑1 (MQ=255)                                                    gCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAg                                                                                                  >  6:281208/1‑148 (MQ=255)                                                       gagGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAAt                                                                                              <  3:226510/149‑1 (MQ=255)                                                         ggTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGa                                                                                            <  6:315157/149‑1 (MQ=255)                                                          gTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGac                                                                                           <  7:265570/149‑1 (MQ=255)                                                             ccAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGacaca                                                                                        <  7:53422/149‑1 (MQ=255)                                                              cAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCCTTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGCGAAG‑A‑GGCCg                                                                                                                     >  6:96795/1‑119 (MQ=14)                                                              cAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCCTTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGCGAAG‑A‑GGCCg                                                                                                                     <  5:96795/119‑1 (MQ=14)                                                                           gcTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCg                                                                          >  2:235410/1‑149 (MQ=255)                                                                               gtggAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCtt                                                                       <  6:121852/148‑1 (MQ=255)                                                                                tggAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgt                                                                     <  6:267417/149‑1 (MQ=255)                                                                                  gcaTGGCTTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGa                                                                   <  2:282786/147‑1 (MQ=255)                                                                                  gAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGa                                                                   <  1:235410/149‑1 (MQ=255)                                                                                   aaTGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAg                                                                  >  2:194581/1‑149 (MQ=255)                                                                                    aTGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGc                                                                         <  4:94530/141‑1 (MQ=255)                                                                                    aTGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGc                                                                         >  3:94530/1‑141 (MQ=255)                                                                                                  aggtGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCa                                                   <  8:122266/146‑1 (MQ=255)                                                                                                      gCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCt                                                <  5:229536/148‑1 (MQ=255)                                                                                                      gCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCt                                                >  6:229536/1‑148 (MQ=255)                                                                                                      gCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGGCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGTAA‑G‑GGGCGTCGAGGTCGATCAAAAAAGGGATGACCCACTCACTTTTTTTGGGTGGTGAGCAAAGGGCGTTCCCCGCtt                                               >  5:185034/1‑149 (MQ=255)                                                                                                          gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAg                                                  >  1:206198/1‑142 (MQ=255)                                                                                                          gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAg                                                  <  2:206198/142‑1 (MQ=255)                                                                                                          gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCAt                                           >  3:222370/1‑149 (MQ=255)                                                                                                           tttGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAATGTGGCGGGGGAGGGCGATCAAAAAAGGAATGACACACTCCCTTTTTTTCCGTTGTGGGCAAGGTGCATTCCACGCtttaa                                            >  1:256580/1‑147 (MQ=255)                                                                                                             tGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGt                                         <  1:194581/148‑1 (MQ=255)                                                                                                                       ttCGCGGCTAAAGCCGCTCCTACCGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCAGa                               >  4:167539/1‑148 (MQ=255)                                                                                                                                 aaGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCa                      <  2:29320/147‑1 (MQ=255)                                                                                                                                 aaGCCGCTCCTACGGGGACCGCGTAGGCGAGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCa                      <  5:165044/147‑1 (MQ=255)                                                                                                                                   gCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCAtt                                                       <  2:169840/112‑1 (MQ=255)                                                                                                                                   gCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCAtt                                                       >  1:169840/1‑112 (MQ=255)                                                                                                                                   gCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAgg                    >  1:291615/1‑147 (MQ=38)                                                                                                                                      gCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAAcc                            <  6:4213/136‑1 (MQ=255)                                                                                                                                      gCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAAcc                            >  5:4213/1‑136 (MQ=255)                                                                                                                                       cgccTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTa              <  2:291615/147‑1 (MQ=255)                                                                                                                                           tACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGa          >  4:198553/1‑149 (MQ=255)                                                                                                                                           tACGGGGACCGCGTAGGCGCGGCTGTAGCCGGGATA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGATCCCAACCTGGAAGCTTGCGa          >  3:200064/1‑149 (MQ=255)                                                                                                                                                    cgcgTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGCCCGcc  >  6:176869/1‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGCCCGCC  >  NC_002947/6004852‑6005146

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑