Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,986,590	A→C	7.4%	intergenic (+79/‑86)	flgA → / → flgM	flagella basal body P‑ring formation protein/flagellin biosynthesis negative regulator FlgM

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,986,590	0	A	C	7.4%	164.3 / 4.1	54	intergenic (+79/‑86)	flgA/flgM	flagella basal body P‑ring formation protein/flagellin biosynthesis negative regulator FlgM
Reads supporting (aligned to +/- strand):  ref base A (21/29);  new base C (2/2);  total (23/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

AACCTCAATTCCAAACGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGGGCGGCGTGCGCGG  >  NC_002947/4986443‑4986734                                                                                                                                                     |                                                                                                                                                 aaCCTCAATTCCAAACGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGa                                                                                                                                                  >  5:220374/1‑148 (MQ=255) aaCCTCAATTCCAAACGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGa                                                                                                                                                  >  1:310117/1‑148 (MQ=255)             aaaCGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATg                                                                                                                                      >  3:217728/1‑148 (MQ=255)              aaCGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGCCTGTCGGCaagccc                                                                                                                                    <  1:1802/149‑5 (MQ=255)              aaCGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCa                                                                                                                                    <  5:25882/149‑1 (MQ=255)                 gcgTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCAtta                                                                                                                                 >  1:115417/1‑148 (MQ=255)                 gcgTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCAtt                                                                                                                                  <  2:115417/148‑1 (MQ=255)                      gTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGcc                                                                                                                            <  4:50925/149‑1 (MQ=255)                      gTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGcc                                                                                                                            >  8:59090/1‑149 (MQ=255)                        cAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCt                                                                                                                           >  1:320760/1‑148 (MQ=255)                          aGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTaaa                                                                                                                        <  4:217728/149‑1 (MQ=255)                          aGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTaaa                                                                                                                        <  5:26085/149‑1 (MQ=255)                              cAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGttt                                                                                                                    <  2:264280/149‑1 (MQ=255)                                gggTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTtat                                                                                                                  <  6:180157/149‑1 (MQ=255)                                       cGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGt                                                                                                           >  4:276972/1‑149 (MQ=255)                                           cctggCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGc                                                                                                       <  7:82167/146‑1 (MQ=255)                                            cGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGcc                                                                                                      <  3:50600/149‑1 (MQ=255)                                                     tCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCATAACACGGGTTCG‑CGGGCTTGCCGACATGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAg                                                                                             <  2:310117/149‑1 (MQ=255)                                                     tCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAg                                                                                             <  4:153559/149‑1 (MQ=255)                                                           tCAGTATGGAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGGTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAACGCAAGc                                                                                       <  2:256198/149‑1 (MQ=255)                                                            cAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGAc                                                                                                                                                 >  2:289478/1‑90 (MQ=255)                                                            cAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGAc                                                                                                                                                 <  1:289478/90‑1 (MQ=255)                                                             aGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGt                                                                                     >  2:248705/1‑149 (MQ=255)                                                             aGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGt                                                                                     >  2:244485/1‑149 (MQ=255)                                                                     cgCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATAc                                                                             <  7:99539/148‑1 (MQ=255)                                                                           ccaccaGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCagag                                                                       >  8:38875/1‑149 (MQ=255)                                                                              ccaGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGtt                                                                    >  6:275887/1‑149 (MQ=255)                                                                              ccaGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGtt                                                                    >  3:286164/1‑149 (MQ=255)                                                                               caGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGtt                                                                    >  8:99454/1‑148 (MQ=255)                                                                                  aTTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTg                                                                <  6:82209/149‑1 (MQ=255)                                                                                        cTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATg                                                          <  7:59090/149‑1 (MQ=255)                                                                                        cTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATg                                                          <  2:147649/149‑1 (MQ=255)                                                                                                     aCCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCGACGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATAATGGTAAACGACtt                                               >  1:52667/1‑148 (MQ=255)                                                                                                     aCCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACtt                                               <  1:172441/147‑1 (MQ=255)                                                                                                     aCCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACtt                                               >  2:172441/1‑147 (MQ=255)                                                                                                        gCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTc                                          <  6:220374/149‑1 (MQ=255)                                                                                                            ttCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTg                                                                >  6:221191/1‑123 (MQ=255)                                                                                                            ttCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTg                                                                <  5:221191/123‑1 (MQ=255)                                                                                                               cTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGaa                                   <  2:320760/149‑1 (MQ=255)                                                                                                                tAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAAt                                                                               >  3:46424/1‑104 (MQ=255)                                                                                                                tAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAAt                                                                               <  4:46424/104‑1 (MQ=255)                                                                                                                tAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGaa                                   >  1:218054/1‑148 (MQ=255)                                                                                                                           aGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCtccgtc                       >  3:97447/1‑149 (MQ=255)                                                                                                                           aGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCtccgt                        <  3:167894/148‑1 (MQ=255)                                                                                                                             aaCACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCtccgtccg                     >  4:239466/1‑149 (MQ=255)                                                                                                                                acGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCa                  <  2:52667/149‑1 (MQ=255)                                                                                                                                       cg‑cgGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATATCTCTCCGTCCGTCACGggcg            <  2:218054/148‑1 (MQ=255)                                                                                                                                        g‑cgGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGggcggc          <  1:248705/149‑1 (MQ=255)                                                                                                                                        g‑cgGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGggcggc          <  1:244485/149‑1 (MQ=255)                                                                                                                                        aaatgcattGCCGCCTGTCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGggc             >  2:33683/8‑147 (MQ=255)                                                                                                                                        aaatgcattGCCGCCTGTCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGggc             <  1:33683/140‑1 (MQ=255)                                                                                                                                        aaatgcattGCCGCCTGTCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGCTTTCTGATCATGGTCATCTACTTCAGTCGTTTGAATAACTCTCCGTCCTTCACGggcgg           >  2:39200/8‑149 (MQ=255)                                                                                                                                           gggCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGGGCGGCGt        <  7:205965/149‑1 (MQ=255)                                                                                                                                             gCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGGGCGGCGTgc      <  3:239466/149‑1 (MQ=255)                                                                                                                                              cTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGGGCGGCGTgcg     >  5:174224/1‑149 (MQ=255)                                                                                                                                                  ccGACAGGCGGCAATGCATTTGTGCCTAAAGGTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGGTTCGGATGATGGTCATCGACTTCAGTCGGTTGATTAACTCTCCGTCCGTCCCGGGCGGCGTGCGCgg  >  2:109364/1‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                 AACCTCAATTCCAAACGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGGGCGGCGTGCGCGG  >  NC_002947/4986443‑4986734

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑