Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,971,954	G→T	13.5%	intergenic (‑389/+28)	PP_4379 ← / ← flgL	3‑oxoacyl‑ACP synthase/flagellar hook‑associated protein FlgL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,971,954	0	G	T	13.5%	134.7 / 13.4	52	intergenic (‑389/+28)	PP_4379/flgL	3‑oxoacyl‑ACP synthase/flagellar hook‑associated protein FlgL
Reads supporting (aligned to +/- strand):  ref base G (26/19);  new base T (3/4);  total (29/23)
Fisher's exact test for biased strand distribution p-value = 6.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.64e-01

GGGCACTGGACCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGTCAGTATCGCCAA  >  NC_002947/4971807‑4972100                                                                                                                                                    |                                                                                                                                                   gggcACTGGACCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTgcg                                                                                                                                                    >  2:143363/1‑148 (MQ=255)   gcACTGGACCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGAAAGGGCTGCgcag                                                                                                                                                 >  1:109156/1‑149 (MQ=255)     aCTGGACCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCgcagca                                                                                                                                               <  2:109156/149‑1 (MQ=255)     aCTGGACCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCAT‑‑CGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCagcagc                                                                                                                                             <  3:287497/149‑1 (MQ=255)          aCCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCTGCGCAGccct                                                                                                                                          <  3:278548/149‑2 (MQ=255)          aCCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGcccc                                                                                                                                          <  4:2332/149‑1 (MQ=255)             ccGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCTGCGCAGccctatc                                                                                                                                       <  5:242291/149‑5 (MQ=255)                aaTGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATc                                                                                                                                    <  1:310064/149‑1 (MQ=255)                 aTGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATca                                                                                                                                   <  3:190259/149‑1 (MQ=255)                    aTCAGCTTCGCAGCAGATGTCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATcagg                                                                                                                                 <  6:40507/148‑1 (MQ=255)                    aTCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATcagg                                                                                                                                 >  5:226591/1‑148 (MQ=255)                        gCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATcaggcagg                                                                                                                             >  1:73312/1‑148 (MQ=255)                               agcagATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGAt                                                                                                                        >  2:29372/1‑146 (MQ=255)                                gcagATATCGATGGGGCCGCATCGCGGCCCTTTCGCCACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGATGACTACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGa                                                                                                                    <  5:306014/149‑1 (MQ=255)                                       tCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTc                                                                                                             <  1:143363/149‑1 (MQ=255)                                         gaaagggCCGCGATGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCg                                                                                                            >  8:134063/5‑148 (MQ=255)                                            ggggCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGaa                                                                                                          >  1:41956/1‑147 (MQ=255)                                             gggCCGCATCGCGGCCCTTTCGAGACGCAAGGACGCTCCCAAGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCGTGTGTCGCGATAGGCCTGCGCAGCAGCCCCAGCATCAGGAAGGCAGATTAGATCTTGTCGAACAg                                                                                                       >  5:31648/1‑149 (MQ=255)                                              ggCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATGAGGCAGGCAGATTAGATCTTGTCGAACAgg                                                                                                      <  1:29372/149‑1 (MQ=255)                                                    aTCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAGTACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGc                                                                                                >  4:43038/1‑149 (MQ=255)                                                     tCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCt                                                                                               >  6:237126/1‑149 (MQ=255)                                                     tCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCt                                                                                               <  4:125877/149‑1 (MQ=255)                                                                tCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATgc                                                                                      <  7:134063/147‑1 (MQ=255)                                                                  gcgACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACa                                                                                                        >  3:147556/1‑127 (MQ=255)                                                                  gcgACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACa                                                                                                        <  4:147556/127‑1 (MQ=255)                                                                    gACGCAAGGCCTCTCCCACCAATACGCCACCTCCAGGAGAGAGGACCACCTGTGGGGGCCTTGTGTCGCGATCGGGCTGCGCAGCAGCCCCAGCATCAGCCAGGCAGAATAGAGCTAGTCCACAACGCATAGCTGAGAAATGCGCGCa                                                                                 >  4:237835/1‑148 (MQ=255)                                                                       gCAAGGCGGCTCCCACGAATACGCCACCTCCATGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAAc                                                                              <  3:237835/148‑1 (MQ=255)                                                                         aaGGCCGCTCCCACGATTACGCCACCTACAGGAGAGAGGACGACCTGTGGTGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGc                                                                            >  7:237640/1‑148 (MQ=255)                                                                         aaGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCCATAGGGCTGCGCAGCAGCCGCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGc                                                                            >  7:242076/1‑148 (MQ=255)                                                                             ccGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGtt                                                                       >  6:245148/1‑149 (MQ=255)                                                                                 tCCCACGAATACGCCACCTCCAGGAGCGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAAGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCg                                                                    >  1:168937/1‑148 (MQ=255)                                                                                   ccACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCa                                                                          <  2:79361/140‑1 (MQ=255)                                                                                   ccACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCa                                                                          >  1:79361/1‑140 (MQ=255)                                                                                   ccACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGaa                                                                  <  5:245148/148‑1 (MQ=255)                                                                                         aTACGCCACCTCCAGGAGAGAGGTCGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTACGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGATCAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTc                                                             >  7:289960/1‑147 (MQ=255)                                                                                                         agagagGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAg                                           >  1:184214/1‑149 (MQ=255)                                                                                                          gagagGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAgg                                          <  5:237126/149‑1 (MQ=255)                                                                                                            gagGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGt                                        >  8:146626/1‑149 (MQ=255)                                                                                                            gagGACGACCTGGGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGt                                        <  2:41956/149‑1 (MQ=255)                                                                                                                  gacCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCt                                   >  4:131822/1‑148 (MQ=255)                                                                                                                    ccTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATTCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGaa                                >  8:170581/1‑149 (MQ=255)                                                                                                                               cTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAg                     >  2:74702/1‑149 (MQ=255)                                                                                                                                ttGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAgg                    >  1:132049/1‑149 (MQ=255)                                                                                                                                   tgtCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTgag                                                                                            >  7:253319/1‑74 (MQ=255)                                                                                                                                   tgtCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTgag                                                                                            <  8:253319/74‑1 (MQ=255)                                                                                                                                     tCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATg               <  6:226591/149‑1 (MQ=255)                                                                                                                                     tCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATg               >  6:162353/1‑149 (MQ=255)                                                                                                                                      gatcctggggCTGCTGCGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGt              >  4:45014/8‑149 (MQ=255)                                                                                                                                        cgATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGTCa            <  3:43038/149‑1 (MQ=255)                                                                                                                                          ctggggCTGCTGCGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCaa                                                           <  4:233085/97‑1 (MQ=255)                                                                                                                                          ctggggCTGCTGCGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCaa                                                           >  3:233085/4‑100 (MQ=255)                                                                                                                                           tggggCTGCTGCGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATgcgc                                                                                    >  6:307111/3‑74 (MQ=38)                                                                                                                                           tggggCTGCTGCGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATgcgc                                                                                    <  5:307111/72‑1 (MQ=38)                                                                                                                                              ggCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGTCAGTATCg      >  7:239414/1‑149 (MQ=255)                                                                                                                                              ggCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGTCAGTATCg      >  2:86374/1‑149 (MQ=255)                                                                                                                                                  gcgcAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGTCAGTATCGCCaa  >  5:228004/1‑149 (MQ=255)                                                                                                                                                   cgcAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGTCAGTATCGCCaa  <  3:287663/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   GGGCACTGGACCCCGAATGATCAGCTTCGCAGCAGATATCGATGGGGCCGCATCGCGGCCCTTTCGCGACGCAAGGCCGCTCCCACGAATACGCCACCTCCAGGAGAGAGGACGACCTGTGGGGGCCTTGTGTCGCGATAGGGCTGCGCAGCAGCCCCAGGATCAGGCAGGCAGATTAGATCTTGTCGAACAGGCTTAGCTGAGAAATGCGCGCAAACGCCAGTTGCGAAGCTTCAAGCATGGCCTGCTGCAGGGTCAGCTGAATGGTGGCCGAGGCCATGTCAGTATCGCCAA  >  NC_002947/4971807‑4972100

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: ‑