Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,615,456	A→G	9.9%	intergenic (+19/‑210)	PP_3186 → / → codB	transcriptional regulator/cytosine transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,615,456	0	A	G	9.9%	127.1 / 3.7	51	intergenic (+19/‑210)	PP_3186/codB	transcriptional regulator/cytosine transporter
Reads supporting (aligned to +/- strand):  ref base A (17/28);  new base G (3/2);  total (21/30)
Fisher's exact test for biased strand distribution p-value = 3.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

AAGCACCTGGATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCGGGTGGCGGCGCA  >  NC_002947/3615309‑3615604                                                                                                                                                      |                                                                                                                                                      aaGCACCTGGATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGAt                                                                                                                                                      <  7:256368/149‑1 (MQ=255) aaGCACCTGGATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGAt                                                                                                                                                      <  1:341039/149‑1 (MQ=255)  aGCACCTGGATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGAtt                                                                                                                                                     <  2:1102/149‑1 (MQ=255)      ccTGGATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATtacta                                                                                                                                                 <  7:123476/149‑1 (MQ=255)       cTGGATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGGTtactac                                                                                                                                                >  2:309464/1‑149 (MQ=255)          gATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCATATGGGGTTGG‑CCGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTAcc                                                                                                                                               <  2:353933/147‑1 (MQ=255)          gATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTAcc                                                                                                                                               >  8:188188/1‑147 (MQ=255)          gATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGGTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTAcc                                                                                                                                               <  1:163167/147‑1 (MQ=255)            tGAACTGGCCGCGCGCAGCAGTTCCGAGCAGCGTTTCGCCGAACTGGCAGGGATTTTTGGCCTGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTAcccagc                                                                                                                                           <  7:301738/149‑1 (MQ=255)              aaCTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTAcccagcc                                                                                                                                          <  4:341971/148‑1 (MQ=255)                   gCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGAc                                                                                                                                    >  7:171681/1‑149 (MQ=255)                   gCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTAGTAATCAcccagcccacgg                                                                                                                                     <  1:232298/148‑4 (MQ=255)                     cgcgcgCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTTGGTGAGTTCAAcccagccccagaacg                                                                                                                                  >  8:79254/1‑142 (MQ=255)                     cgcgcgCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCg                                                                                                                                  <  2:208908/149‑1 (MQ=255)                          gcagcaTGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTg                                                                                                                            >  8:102319/1‑149 (MQ=255)                            agcaTGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGt                                                                                                                          <  1:336367/149‑1 (MQ=255)                            agcaTGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGt                                                                                                                          <  7:188188/149‑1 (MQ=255)                            agcaTGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGt                                                                                                                          <  6:118924/149‑1 (MQ=255)                              caTGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGTTGATTACTACCCAGCCCAGGACCGC‑TTTGGt                                                                                                                          <  1:226471/147‑1 (MQ=255)                                      agcagcGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑ATTGGTGCATTGgggc                                                                                                                >  7:280785/1‑149 (MQ=255)                                      agcagcGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCGGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGgcgc                                                                                                                <  5:346818/149‑1 (MQ=255)                                                   cGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGGTTTCTACCCCGCCCAGGTCCGC‑ATTGGTGCATGGGGGCCTCAAAAAAAgtc                                                                                                   >  8:317274/1‑149 (MQ=255)                                                          gCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGc                                                                                            <  1:149062/149‑1 (MQ=255)                                                          gCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTCGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGc                                                                                            >  7:82834/1‑149 (MQ=255)                                                          gCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCGGGCAAATGGGGTTGGAATGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACAGC‑ATTGGTGGATGGGCGCCAAAAAATAAGTCGTCCCg                                                                                             >  1:108614/1‑149 (MQ=255)                                                            aGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCCGGCCCGC‑TTTTGTGCATGGGCGGCTGAAAATAAGTAGTCCCGcac                                                                                          >  3:274765/1‑149 (MQ=255)                                                            aGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCAGGGTGATTACATCCCACCCCACGGCCGC‑TTTGGTGCATGGGCGCCGCAAAATAAGTAGTCCCGccc                                                                                          >  3:212155/1‑147 (MQ=255)                                                                 tttttGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGCCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTcc                                                                                     <  3:203810/149‑1 (MQ=255)                                                                     tGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACAGCCGTGGGCTGGCTGCTTACTTCCCAGGCCACGACCGC‑GTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCCCACTCCAg                                                                                   >  3:51616/1‑147 (MQ=255)                                                                         cAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGGTTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTc                                                                             <  1:309464/149‑1 (MQ=255)                                                                         cAGGCCCCCTGCCTGGTGGGTGTTTTCGGGCAAA‑GGGGTTGG‑CTCGGCCCGTTGTAAACCGCGGTGGGCTGGGTTATTACAACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTc                                                                             <  6:255446/149‑1 (MQ=255)                                                                             ccTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCCGCCCCGGCCCCC‑TTTGGTGCATGGGCGGCTCAAAATAAGTCGTCCCGCCCCCTCCCGATCGTCAgct                                                                         >  7:36752/1‑147 (MQ=255)                                                                              cTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGGGATTACTACCCCGCCCCCGACCGC‑GTTTGTGCCTGGGCGCCACAAAAAAAGTAGTCCCGCCCACTCCAGCACGTCAGCTc                                                                        >  5:223821/1‑149 (MQ=255)                                                                                     cTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTAATACCCAGCCCACGACCGC‑ATTTGTGCATGGGCGCCTCAAAAAAAATCGTCCCCCACACAACACATCGTGAGATCGCAGcat                                                                 >  5:8843/1‑147 (MQ=255)                                                                                           gCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTTCTACCCAGCCCCGGACCGC‑TTTTGTGCATTGGCGGCTCAAAATAAGTAGTGCCGCACACTACACATAGTCAGATAGCAGCATTAAttt                                                           >  1:271725/1‑147 (MQ=255)                                                                                           gCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAAtgt                                                           <  7:79254/149‑1 (MQ=255)                                                                                                    tGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGGAGGGGGATTAATACCCAGCCCAGGACCGC‑GTTGGTGCATGGGGGCCTCAAAATAAGTAGTACCCCACCCAACAGAACGGAAGCTAGCAGCATTAAtttggccactg                                                   >  4:144563/1‑141 (MQ=255)                                                                                                      gCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCat                                                <  1:159008/149‑1 (MQ=255)                                                                                                        aaaTGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCatat                                              <  7:317274/149‑1 (MQ=255)                                                                                                                     aCGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGc                                  <  8:82834/149‑1 (MQ=255)                                                                                                                      cGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGTCg                                 <  6:301309/149‑1 (MQ=255)                                                                                                                               tgtAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGCCCGCTTTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGcc                          >  1:93992/1‑149 (MQ=255)                                                                                                                                   aaCCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCaaaa                                                                                                         <  3:310898/65‑1 (MQ=255)                                                                                                                                    aCCGCCGTGGTCTGGTTGATTACTACCCAGCGCAGGACCGC‑TTTGGTGAATGGTCGCCTCAAAATACGTCGTCCAGCACACTCCCGATCGGCAGATCTGAGCTTTTATGTGCACAGTGCATATGGATTTCTGGGCGAAGAGCCCGAtt                     <  3:200898/148‑1 (MQ=255)                                                                                                                                      cgccgTGGGCTTGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATTTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATttct                  <  8:171681/149‑1 (MQ=255)                                                                                                                                         cgTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGCGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTcc               <  7:98734/149‑1 (MQ=255)                                                                                                                                           tGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCgg             <  4:164541/149‑1 (MQ=255)                                                                                                                                           tGGGCTGGGTAGTAATCACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCgg             >  4:36143/1‑149 (MQ=255)                                                                                                                                             ggCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCTCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCggg            <  2:108614/148‑1 (MQ=255)                                                                                                                                               cTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCGGGTgg         >  3:4070/1‑149 (MQ=255)                                                                                                                                                  ggTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCGGGTggcgg      >  5:76943/1‑149 (MQ=255)                                                                                                                                                      aTTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCGGGTGGCGGCGCa  <  8:280785/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                      AAGCACCTGGATGAACTGGCCGCGCGCAGCATGACCGAGCAGCGGTTCGCCGAACTGGCAGGGATTTTTGGCCAGGCCTCCAGCCTGGAGGCGGATTTCTGGCAAATGGGGTTGG‑ACGGGACCG‑TGTAAACCGCCGTGGGCTGGGTGATTACTACCCAGCCCAGGACCGC‑TTTGGTGCATGGGCGCCTCAAAATAAGTCGTCCCGCACACTCCAGATCGTCAGATCGCAGCTTTAATGTGCACAGTGCATATGGATTTCTGGGCGAACAGCCCGATTTCTTCCGGGTGGCGGCGCA  >  NC_002947/3615309‑3615604

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: ‑