Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,637,325	A→T	7.8%	intergenic (+34/+32)	pdxJ → / ← PP_1437	pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,637,325	0	A	T	7.8%	143.8 / 2.3	51	intergenic (+34/+32)	pdxJ/PP_1437	pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base A (23/24);  new base T (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

CAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGT  >  NC_002947/1637186‑1637473                                                                                                                                             |                                                                                                                                                      cAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCTTGCCcgcg                                                                                                                                               >  4:241964/1‑148 (MQ=255)    tGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCTTGCCCGCGaaaa                                                                                                                                           <  3:241964/149‑3 (MQ=255)    tGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGaa                                                                                                                                             >  1:285123/1‑147 (MQ=255)    tGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAaga                                                                                                                                           <  3:242508/149‑1 (MQ=255)             cATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGca                                                                                                                                  >  7:231263/1‑148 (MQ=255)             cATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGca                                                                                                                                  >  6:58879/1‑148 (MQ=255)              aTTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGcaca                                                                                                                                >  8:220718/1‑149 (MQ=255)              aTTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTAGCGCTGATTGTTGGTCTCATTTA‑CCGGCCTTTTCTCGGGCAATCCCGCGAAGAGG‑CCAGca                                                                                                                                  >  8:224969/1‑147 (MQ=255)                tGGCCATGCGCTGGTGGCGCATGCCTTGTTTGACGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAgg                                                                                                                              >  6:327388/1‑149 (MQ=255)                  gCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAgg                                                                                                                                         <  8:95849/137‑1 (MQ=255)                  gCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAgg                                                                                                                                         >  7:95849/1‑137 (MQ=255)                       gcgcTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTCGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGa                                                                                                                       >  6:245949/1‑149 (MQ=255)                         gcTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGAt                                                                                                                      >  1:213607/1‑148 (MQ=255)                          cTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCa                                                                                                                    <  5:268431/149‑1 (MQ=255)                                  gcATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGTCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGca                                                                                                                                  >  1:70968/1‑127 (MQ=255)                                  gcATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGTCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGca                                                                                                                                  <  2:70968/127‑1 (MQ=255)                                  gcATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGTTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGa                                                                                                                       >  7:166515/1‑138 (MQ=255)                                  gcATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGTTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGa                                                                                                                       <  8:166515/138‑1 (MQ=255)                                  gcATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAg                                                                                                            <  2:285123/149‑1 (MQ=255)                                    aTGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTACCCGGCCTTTTCGCGGGCAAGCCCGCGAaga                                                                                                                                           <  1:191976/118‑1 (MQ=255)                                    aTGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAaga                                                                                                                                           >  2:191976/1‑117 (MQ=255)                                        cTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGaa                                                                                                         <  1:299722/146‑1 (MQ=255)                                        cTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGaa                                                                                                         >  2:299722/1‑146 (MQ=255)                                         ttgtttgtCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAggc                                                                                                                             <  4:112499/125‑1 (MQ=255)                                         ttgtttgtCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAggc                                                                                                                             >  3:112499/1‑125 (MQ=255)                                         ttgtttgtCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAacac                                                                                                     >  6:135067/1‑149 (MQ=255)                                                        aaGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCggg                                                                                       <  2:213607/148‑1 (MQ=255)                                                        aaGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGt                                                                                      <  5:58879/149‑1 (MQ=255)                                                         aGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTa                                                                                     <  7:224969/149‑1 (MQ=255)                                                         aGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTa                                                                                     <  7:220718/149‑1 (MQ=255)                                                                    gCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAggg                                                                           <  5:135067/148‑1 (MQ=255)                                                                     ccGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAggggg                                                                         <  5:327388/149‑1 (MQ=255)                                                                     ccGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAggggg                                                                         >  3:140326/1‑149 (MQ=255)                                                                       gagaTGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAggggg                                                                         >  7:148489/1‑147 (MQ=255)                                                                         gaTGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTCGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAgc                                                                     <  5:245949/149‑1 (MQ=255)                                                                             aaGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAgctgct                                                                 <  6:105328/149‑1 (MQ=255)                                                                                                           ttgttgGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCAt                                   >  6:191375/1‑149 (MQ=255)                                                                                                                ggTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATc                               <  8:231263/148‑1 (MQ=255)                                                                                                                     ccTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTc                         <  4:140326/149‑1 (MQ=255)                                                                                                                      cTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGCTCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCa                        >  5:38455/1‑149 (MQ=255)                                                                                                                      cTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCa                        <  8:148489/149‑1 (MQ=255)                                                                                                                            ccGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTTCTGACCTCGACACGCCCGCCATGCAAATGCATGATCGACTTCACGATc                   >  2:289937/1‑149 (MQ=255)                                                                                                                             cGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGTCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACATCGACCCGCCCGCCATGCAAc                                        >  1:34573/1‑128 (MQ=255)                                                                                                                             cGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAAc                                        <  2:34573/127‑1 (MQ=255)                                                                                                                                  tcttCGCGGGCTTGCCCGCGAAAAGG‑CCGGTACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGAcccgccc                                                  <  1:109246/110‑1 (MQ=37)                                                                                                                                  tcttCGCGGGCTTGCCCGCGAAAAGG‑CCGGTACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGAcccgccc                                                  >  2:109246/3‑112 (MQ=37)                                                                                                                                       gcgGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGccaaccccaa        >  6:79810/1‑149 (MQ=255)                                                                                                                                        cgGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGccaaccccaac       <  6:38455/149‑1 (MQ=255)                                                                                                                                        cgGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGccaaccccaac       <  5:191375/149‑1 (MQ=255)                                                                                                                                          ggCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGt                                                                                      >  5:250416/1‑68 (MQ=255)                                                                                                                                          ggCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGt                                                                                      <  6:250416/68‑1 (MQ=255)                                                                                                                                             aaGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGt  >  1:15508/1‑149 (MQ=255)                                                                                                                                             |                                                                                                                                                      CAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCTTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTGTTGGTCGCCTGTA‑CCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGG‑CCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGACTTCACGATCGCCAACCCCAACCCGGT  >  NC_002947/1637186‑1637473

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: ‑