Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,004,973	G→C	11.1%	intergenic (+11/‑165)	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	6,004,973	0	G	C	11.1%	152.7 / 10.3	54	intergenic (+11/‑165)	PP_5259/ydcJ	LysR family transcriptional regulator/metalloprotein
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base C (3/3);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.13e-01

GGTAGCCTGGTGGTGCCGTGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGA  >  NC_002947/6004828‑6005117                                                                                                                                                   |                                                                                                                                                   ggTAGCCTGGTGGTGCCGTGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCgg                                                                                                                                                 <  4:189712/149‑1 (MQ=255)      ccTGGTGGTGCCGTGGAACCATGCAATGCGCAGTGCCGGAGCGCACTTAACTGCCCAATGCCGATCATGCGGCAGAGGTGCCAAAGCTGCGGGCGCTGGTCGAATGGATTGGCGAGCAGTTGCAGGATTGACGGCCTCTTCGCggatt                                                                                                                                              >  1:225150/1‑145 (MQ=255)      ccTGGTGGTGCCGTGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTaaa                                                                                                                                            <  5:73738/149‑1 (MQ=255)       cTGGTGGTGCCGTGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAg                                                                                                                                           >  4:264344/1‑149 (MQ=255)               gCCGTGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTcc                                                                                                                                    >  1:277017/1‑148 (MQ=255)                ccGTGGAACGATGCAATGCGCAGTGGCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGTCAGAGGTGCCATAGGTGGGGGCGCTGGTTGAATGGATTGGCGAGCTGTTGGAGGTTTGACGGCCTCTTCGCGGCTTTAGCCGcgaaga                                                                                                                                  <  2:225150/149‑6 (MQ=255)                  gTGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCCTTTCCCGGCTAAAGCCGCGCCTACg                                                                                                                                >  4:197700/1‑149 (MQ=255)                   tGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGAGGGCGCTGGTGGAATGGATTGGCGAGCAGGTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTACTACgg                                                                                                                               >  5:237482/1‑149 (MQ=255)                       aCCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGAc                                                                                                                           >  6:105077/1‑149 (MQ=255)                        ccATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGAcc                                                                                                                          <  3:264344/149‑1 (MQ=255)                         cATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACcg                                                                                                                         >  6:165044/1‑149 (MQ=255)                         cATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCCGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTAGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACcg                                                                                                                         >  1:29320/1‑149 (MQ=255)                          aTGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAg                                                                                                                                           <  8:186463/130‑1 (MQ=255)                          aTGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAg                                                                                                                                           >  7:186463/1‑130 (MQ=255)                             cAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTa                                                                                                                     <  5:105077/149‑1 (MQ=255)                                  cgcAGTGGCGGTGCGGA‑TTACCTGGCGTATGCCGTGGATGGGGCAGAGGTGCCAATGGTGCGTGCGCTGGTGGAATGGATTGGCGAGGAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGgcgc                                                                                                                <  2:88086/149‑1 (MQ=255)                                       tGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGTGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCtt                                                                                                           <  8:3829/149‑1 (MQ=38)                                         ccGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCtt                                                                                                           >  8:265570/1‑147 (MQ=255)                                              gcgcA‑TTACCTGGCGTATGCCGAGCCTGCGGCAGAGGTGCCAACGGTGCGGGCGCTGGTGGAATGGATTGGCTAGCAGTTGCAGGGTTGACGGCCTCTTCGCGGCTAACGCCGCTCCTCCGGTGACCGCGTAGGCGCGGCTTTAGCCgg                                                                                                    <  1:75527/149‑1 (MQ=255)                                              gcgcA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCCTTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCgc                                                                                                    <  3:197700/149‑2 (MQ=25)                                                 cA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGa                                                                                                  >  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                                                                                        <  5:96795/119‑1 (MQ=14)                                                                                       cAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCCTTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGCGAAG‑A‑GGCCg                                                                                        >  6:96795/1‑119 (MQ=14)                                                                                                 ggCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTAGCGGCTAAAGCCGCTCCTACGGGGAc                                                                                                                           >  4:102904/1‑76 (MQ=255)                                                                                                 ggCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTAGCGGCTAAAGCCGCTCCTACGGGGAc                                                                                                                           <  3:102904/76‑1 (MQ=255)                                                                                                    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                   >  6:229536/1‑148 (MQ=255)                                                                                                                               gCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCt                   <  5:229536/148‑1 (MQ=255)                                                                                                                               gCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGGCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGTAA‑G‑GGGCGTCGAGGTCGATCAAAAAAGGGATGACCCACTCACTTTTTTTGGGTGGTGAGCAAAGGGCGTTCCCCGCtt                  >  5:185034/1‑149 (MQ=255)                                                                                                                                   gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAg                     <  2:206198/142‑1 (MQ=255)                                                                                                                                   gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAg                     >  1:206198/1‑142 (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)                                                                                                                                                   |                                                                                                                                                   GGTAGCCTGGTGGTGCCGTGGAACCATGCAATGCGCAGTGCCGGAGCGCA‑TTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAA‑G‑GGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGA  >  NC_002947/6004828‑6005117

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: ‑