Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,986,594	G→T	7.7%	intergenic (+83/‑82)	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	4,986,594	0	G	T	7.7%	153.1 / 2.8	52	intergenic (+83/‑82)	flgA/flgM	flagella basal body P‑ring formation protein/flagellin biosynthesis negative regulator FlgM
Reads supporting (aligned to +/- strand):  ref base G (20/28);  new base T (2/2);  total (22/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01

AAACGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGGGCGGCGTGCGCGG  >  NC_002947/4986455‑4986734                                                                                                                                             |                                                                                                                                             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                                                                                                                        <  5:26085/149‑1 (MQ=255)              aGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTaaa                                                                                                                        <  4:217728/149‑1 (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)                                                 aGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGt                                                                                     >  2:244485/1‑149 (MQ=255)                                                 aGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGt                                                                                     >  2:248705/1‑149 (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                                               >  2:172441/1‑147 (MQ=255)                                                                                         aCCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACtt                                               <  1:172441/147‑1 (MQ=255)                                                                                            gCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTc                                          <  6:220374/149‑1 (MQ=255)                                                                                                ttCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTg                                                                <  5:221191/123‑1 (MQ=255)                                                                                                ttCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTg                                                                >  6:221191/1‑123 (MQ=255)                                                                                                   cTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGaa                                   <  2:320760/149‑1 (MQ=255)                                                                                                    tAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAAt                                                                               <  4:46424/104‑1 (MQ=255)                                                                                                    tAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAAt                                                                               >  3:46424/1‑104 (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             <  1:33683/140‑1 (MQ=255)                                                                                                                            aaatgcattGCCGCCTGTCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGggc             >  2:33683/8‑147 (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)                                                                                                                                             |                                                                                                                                             AAACGCGTGGTCAAGGCCAGGGTGACCGGCCCGGGCCAGGTCGAGGTCAGTATGTAGGCTAGCCACCAGATTGCGCTGGCAGTGAGGAACCGCTTTTCCTAAACTGTGTCAGAACACGGGTTCG‑CGGGCTTGCCGACAGGCGGCAATGCATTTGTGCCTAAAGTTTATATCGGGTTGGCCGAAAACAAGGCAAGCGTCCAAATACCCAGAGGTTTCTGATCATGGTCATCGACTTCAGTCGTTTGAATAACTCTCCGTCCGTCACGGGCGGCGTGCGCGG  >  NC_002947/4986455‑4986734

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: ‑