Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,955,210	T→A	11.3%	intergenic (+40/‑153)	PP_1752 → / → PP_1753	hypothetical protein/DMT superfamily permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,955,210	0	T	A	11.3%	140.8 / 7.9	53	intergenic (+40/‑153)	PP_1752/PP_1753	hypothetical protein/DMT superfamily permease
Reads supporting (aligned to +/- strand):  ref base T (22/25);  new base A (3/3);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

CCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGGCTTGATC  >  NC_002947/1955065‑1955353                                                                                                                                                  |                                                                                                                                                 cccTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTAcc                                                                                                                                               <  4:166387/149‑1 (MQ=255)    ttGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCcgc                                                                                                                                            >  3:59923/1‑149 (MQ=255)      ggACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCcgcg                                                                                                                                           >  3:265890/1‑148 (MQ=255)         cGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTAAACCCGCGaagc                                                                                                                                       <  3:332615/149‑3 (MQ=255)          gCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAgg                                                                                                                                      <  1:226777/149‑1 (MQ=255)              gtggAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTGCTGACCCTTTCGCGGGTAAACCCGCGaagcggc                                                                                                                                    <  5:113653/147‑6 (MQ=38)                 gAGGCCAATGACAAGCGCTGGGCGCGGGTTAAGGAGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGca                                                                                                                               >  6:176520/1‑149 (MQ=255)                   ggCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGcaca                                                                                                                             <  4:28184/149‑1 (MQ=255)                     ccAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAgg                                                                                                                           <  3:104765/149‑1 (MQ=255)                      cAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAgg                                                                                                                           >  8:193225/1‑148 (MQ=255)                         tGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAa‑c                                                                                                                      <  4:265890/149‑1 (MQ=255)                             aaGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCt                                                                                                                  >  1:313716/1‑149 (MQ=255)                              aGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTc                                                                                                                 <  4:59923/149‑1 (MQ=255)                                    gggCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCAcc                                                                                                             >  5:143912/1‑147 (MQ=255)                                        gcgGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCa                                                                                                       <  7:193225/149‑1 (MQ=255)                                           ggTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGc                                                                                                    <  2:313716/149‑1 (MQ=255)                                           ggTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGc                                                                                                    <  5:347860/149‑1 (MQ=255)                                                aGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCa                                                                                                >  6:8838/1‑148 (MQ=255)                                                  cctgtgCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCaaaa                                                                                             <  5:299367/146‑1 (MQ=255)                                                     gtgCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGaa                                                                                          <  5:8838/149‑1 (MQ=255)                                                        cgcACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGt                                                                                                                                    <  6:47085/105‑1 (MQ=255)                                                        cgcACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACCACCTCCACCCAGCCATGCCCCAAAAGAAt                                                                                         <  1:213419/148‑1 (MQ=255)                                                         gcACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGAc                                                                                      <  6:143912/149‑1 (MQ=255)                                                          cacaATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAATAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTGCGCGGGTTTACCCGCGAAAGGGTCAGc                                                                                                                                <  5:15615/107‑1 (MQ=255)                                                             aaTCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtg                                                                                   >  4:26832/1‑148 (MQ=255)                                                              aTCAACCAGGCGCTTGAGGCGGTGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtgat                                                                                 <  5:4039/149‑1 (MQ=255)                                                               tCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtgat                                                                                 >  1:222472/1‑148 (MQ=255)                                                               tCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtgat                                                                                 <  2:222472/148‑1 (MQ=255)                                                                   ccAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAAt                                                                             >  5:73883/1‑148 (MQ=255)                                                                          cTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGATGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTtct                                                                     <  3:26832/149‑1 (MQ=255)                                                                                gcggcgTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCTCAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCAc                                                               >  4:176840/1‑149 (MQ=255)                                                                                   gcgTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtga                                                                                  <  5:113480/127‑1 (MQ=255)                                                                                   gcgTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtga                                                                                  >  6:113480/1‑127 (MQ=255)                                                                                            aaGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtgat                                                                                 >  1:236644/1‑119 (MQ=255)                                                                                            aaGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCtgat                                                                                 <  2:236644/119‑1 (MQ=255)                                                                                                  aaGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGtc                                              >  4:193189/1‑148 (MQ=255)                                                                                                    gAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTctct                                                 >  4:90570/1‑143 (MQ=255)                                                                                                    gAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTctct                                                 <  3:90570/143‑1 (MQ=255)                                                                                                          gCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAAccc                                     >  5:279683/1‑149 (MQ=255)                                                                                                           ccGAAGGTGAGGTTGCCTGTTCTGGCCGCTACGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAAcccc                                    >  1:32085/1‑149 (MQ=255)                                                                                                                   gAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGtcc                                             >  1:338929/1‑132 (MQ=255)                                                                                                                   gAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGtcc                                             <  2:338929/132‑1 (MQ=255)                                                                                                                     ggTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTc                           >  2:220180/1‑148 (MQ=255)                                                                                                                         gCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTcaacaa                      >  8:233638/1‑149 (MQ=255)                                                                                                                           cTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCAACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAAcc                    <  5:176520/149‑1 (MQ=255)                                                                                                                                cTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCccac               >  3:198799/1‑149 (MQ=255)                                                                                                                                      ctttCGCGGGTAAACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACggg         >  5:210684/3‑149 (MQ=255)                                                                                                                                        ttCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGGCt       >  3:137880/1‑149 (MQ=255)                                                                                                                                          cgcgGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGGCt       <  3:193189/147‑1 (MQ=255)                                                                                                                                           gcgGGTAAACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCaacaac                     <  7:276963/132‑1 (MQ=255)                                                                                                                                           gcgGGTAAACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCaacaac                     >  8:276963/1‑132 (MQ=255)                                                                                                                                            cgGGTAAACCCGCGAAGCGGCCAGAACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGGCTTGAt   >  2:265146/1‑149 (MQ=255)                                                                                                                                             gggTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGGCTTGATc  <  6:279683/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                 CCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCAAGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAA‑CACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGGCTTGATC  >  NC_002947/1955065‑1955353

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: ‑