Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,637,299	T→C	9.4%	intergenic (+8/+58)	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	1,637,299	0	T	C	9.4%	138.7 / 5.0	53	intergenic (+8/+58)	pdxJ/PP_1437	pyridoxine 5'‑phosphate synthase/heavy metal sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base T (23/25);  new base C (3/2);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.27e-01

CAACGTCGAGGCGGTGGCGGCGATCAAGGGTATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGA  >  NC_002947/1637153‑1637446                                                                                                                                                     |                                                                                                                                                    caACGTCGAGGCGGTGGCGGCGATCAAGGGTATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCg                                                                                                                                                   >  4:309026/1‑149 (MQ=255)                   ggcgATCAAGGGTATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCTGTGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTc                                                                                                                                  >  1:263160/1‑149 (MQ=255)                   ggcgATCAAGGGTATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TCGGCCGCCTGTGCTGGCCTCTTcg                                                                                                                                 >  4:92119/1‑149 (MQ=255)                         cAAGGGTATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCCGAGTGATCGGCCGCCTGTGCTGGCCTCTTCGCGGGc                                                                                                                            >  6:317772/1‑149 (MQ=38)                               tATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCggg                                                                                                                             >  8:85036/1‑141 (MQ=255)                               tATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCggg                                                                                                                             <  7:85036/141‑1 (MQ=255)                               tATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGATTCAATGCTGCTGTGCCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATAG‑TTGGTCGCCTGTACCGGACTTTTCGCGGGCAAGCCcg                                                                                                                     >  5:113991/1‑149 (MQ=255)                                    aTGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAag                                                                                                                <  5:73485/149‑1 (MQ=255)                                     tGAGTTGAACCTTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTAAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAaga                                                                                                               <  5:248602/149‑1 (MQ=255)                                     tGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCTTGCCCGCGaaaa                                                                                                               <  7:93395/149‑3 (MQ=255)                                     tGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTCTTCGCGGGCTTGCCCGCGaaaa                                                                                                               <  8:314554/149‑3 (MQ=255)                                       aGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCTTGCCCGCGAaaag                                                                                                              <  3:140429/148‑1 (MQ=255)                                       aGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCCGAGTGATCGGCCGCCTGTGCTGGCCTCTTCGCGGGCTTGCCCGCGAaaag                                                                                                              <  5:317772/149‑1 (MQ=25)                                           gAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCa                                                                                                          <  1:201394/148‑1 (MQ=255)                                           gAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAg                                                                                                         >  1:183594/1‑149 (MQ=255)                                            aaCATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTGCTGGCCTCTTCGCGGGCTTGCCCGCGAAAAGGccgg                                                                                                         >  6:73722/1‑146 (MQ=38)                                             aCATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGca                                                                                                       >  3:188429/1‑149 (MQ=255)                                               aTTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGc                                                                                                                            <  2:173094/126‑1 (MQ=255)                                                  ggCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TCGGCCGCCTGTGCTGGCCTCTTCGCGGGCTTGCCCGCGAAAAGGCCGGTACAggc                                                                                                  >  2:180775/1‑149 (MQ=25)                                                     cATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTTTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGTTTG‑TTGGTCGCCTGTAGCGGCCTTATCGCGGGCTAGCCCGCGAAGAGGCCAGCACAggcggc                                                                                               <  6:113991/149‑1 (MQ=255)                                                      aTGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGcc                                                                                              >  4:211487/1‑149 (MQ=255)                                                         cgcTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTGCTGGCCTCTTCGCGGGCTTGCCCGCGAAAAGGCCGGTACAGGCGAccaa                                                                                            <  5:73722/148‑3 (MQ=25)                                                         cgcTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGa                                                                                            <  2:183594/148‑1 (MQ=255)                                                          gcTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TCGGCCGCCTGTGCTGGCCTCTTCGCGGGCTTGCCCGCGAAAAGGCCGGTACAGGCGAccaaca                                                                                          <  1:180775/149‑5 (MQ=21)                                                                   gcATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAg                                                                                 >  4:268027/1‑149 (MQ=255)                                                                                tgtCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAgg                                                                      <  3:309026/148‑1 (MQ=255)                                                                                 gtCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAggg                                                                     <  8:150716/148‑1 (MQ=255)                                                                                         cAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCggg                                                            >  1:242889/1‑149 (MQ=255)                                                                                          aaGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCggg                                                            >  4:109841/1‑148 (MQ=255)                                                                                           tggCTGGTGTGGCCGAGATGAAGGCTCTGATCGTGGCGGCTTCGCGGTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCTGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTa                                                          <  3:192643/148‑1 (MQ=255)                                                                                             gctgctGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAgg                                                        >  3:256957/1‑149 (MQ=255)                                                                                                    tgGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCa                                                   <  3:109841/147‑1 (MQ=255)                                                                                                      gCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAggg                                                <  2:263160/148‑1 (MQ=255)                                                                                                       ccGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAggggg                                              >  1:265025/1‑149 (MQ=255)                                                                                                        cGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAggggg                                              >  4:159733/1‑148 (MQ=255)                                                                                                          agaTGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAaga                                                                                                               >  6:271273/1‑81 (MQ=255)                                                                                                          agaTGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAaga                                                                                                               <  5:271273/81‑1 (MQ=255)                                                                                                              gAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAgctgc                                       >  5:177783/1‑149 (MQ=255)                                                                                                                  gcgcTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGAc                                   <  4:256957/149‑1 (MQ=255)                                                                                                                  gcgcTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGAc                                   >  5:203766/1‑149 (MQ=255)                                                                                                                    gcTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCt                                 <  3:159733/149‑1 (MQ=255)                                                                                                                        aTCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGAc                             <  4:188429/149‑1 (MQ=255)                                                                                                                         tCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGAcc                            <  3:268027/149‑1 (MQ=255)                                                                                                                                ggcTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAgggg                                               >  2:309265/1‑123 (MQ=255)                                                                                                                                ggcTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAgggg                                               <  1:309265/123‑1 (MQ=255)                                                                                                                                   ttCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCAt                  >  4:328879/1‑149 (MQ=255)                                                                                                                                      gcgcTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGc                >  1:326217/1‑148 (MQ=255)                                                                                                                                       cgcTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCaa              <  3:211487/149‑1 (MQ=255)                                                                                                                                         cTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACt            <  2:242889/149‑1 (MQ=255)                                                                                                                                            aTTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCa         >  3:314413/1‑149 (MQ=255)                                                                                                                                             ttg‑ttgGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCAt        >  6:183018/1‑149 (MQ=255)                                                                                                                                               g‑ttgGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATg       <  6:177783/148‑1 (MQ=255)                                                                                                                                                    gTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGa  >  3:269715/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                    CAACGTCGAGGCGGTGGCGGCGATCAAGGGTATCAATGAGTTGAACATTGGCCATGCGCTGGTGGCGCATGCCT‑TGTTTGTCGGCTTCAAGGCTGCTGTGGCCGAGATGAAGGCGCTGATCGTGGCGGCTTCGCGCTGATTG‑TTGGTCGCCTGTACCGGCCTTTTCGCGGGCAAGCCCGCGAAGAGGCCAGCACAGGCGGCCGATCACTCGGCAGGAAACACCAGGGTAAACCGGGTAGGCCCCAGGGGGCAGCTGCTGACCTCGACCCGCCCGCCATGCAACTGCATGATCGA  >  NC_002947/1637153‑1637446

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: ‑