Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,945,358	T→C	12.9%	intergenic (+718/+80)	PP_5673 → / ← flhB	D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,945,358	0	T	C	12.9%	131.1 / 10.1	54	intergenic (+718/+80)	PP_5673/flhB	D‑alanine‑‑D‑alanine ligase/flagellin export apparatus substrate specificity protein
Reads supporting (aligned to +/- strand):  ref base T (32/15);  new base C (4/3);  total (36/18)
Fisher's exact test for biased strand distribution p-value = 6.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GCAAGCTCGCTCCTACATTTGTTTCGGGCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGGCGCTTGCCCT  >  NC_002947/4945216‑4945505                                                                                                                                               |                                                                                                                                                     gCATGCGCGCTCCTAATTTTGTTTCGGGCCTGTTATTCCGGCGGTTTTTACGCGCGACCGCCTGCGCTTACACCTCCATATGGCGCCTTACAACCAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGga                                                                                                                                                <  6:83031/149‑1 (MQ=21)    aGCTCGCTCCTACATTTGTTTCGGGCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGgagcg                                                                                                                                             >  3:87411/1‑149 (MQ=255)        cgctcCTACATTTGTTTCGGGCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACACGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTa                                                                                                                                                   <  6:167101/139‑1 (MQ=255)        cgctcCTACATTTGTTTCGGGCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTa                                                                                                                                                   >  5:167101/1‑139 (MQ=255)         gctcCTACATTTGTTTAGGGCCAGTTATTCATGCTGGATTTACGCGCGAACGCCTTCGCGTACAACTAGATATTGCGCCGTACAAACAAGGCGGTCGCGAGCGCCGGGCACAGGAGGGACTGGCACGAAACAAATGTAGGAGCGAGCtt                                                                                                                                        >  8:235073/1‑149 (MQ=25)              tACATTTGTTTGGGGCATTTTTTTCGTGCGGTTTTAACGCGCGACCGCCTGCGCTACCCCCTCCATATTGCGCTGTACAAACACGGCGGTGGGGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTcg                                                                                                                                   <  4:81032/149‑1 (MQ=21)                     gTTTCGGGCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATgcg                                                                                                                            >  8:277619/1‑149 (MQ=255)                      tttCGGGCCATTAATTCCGCCGGGATTTACGCGCGACCCCCTTCGCTTACACCTCGATATTGCCCCGTACAAACATGGCGGGCGGGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATgcg                                                                                                                            <  4:87411/148‑1 (MQ=37)                        tCGGGCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCAATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGcgccg                                                                                                                         >  1:98027/1‑149 (MQ=255)                          gggCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCcgcg                                                                                                                       >  1:301326/1‑149 (MQ=255)                           ggCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCcgcgc                                                                                                                      >  1:172580/1‑149 (MQ=255)                                       cTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGTAAATCCCGCAGGAATAACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTc                                                                                                          >  2:257326/1‑148 (MQ=17)                                       cTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCcgcgc                                                                                                                      >  1:349022/1‑137 (MQ=255)                                       cTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTc                                                                                                          >  3:374984/1‑148 (MQ=255)                                        tGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGa                                                                                                        >  5:34673/1‑149 (MQ=255)                                                 tACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAg                                                                                                >  3:285195/1‑148 (MQ=255)                                                 accgcgcgACCCCCTTCGCGTACACCTCGATATTGCGCCTTACAACCATGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAg                                                                                                <  4:285195/146‑1 (MQ=255)                                                      gcgACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACg                                                                                          >  7:224779/1‑149 (MQ=255)                                                           cGCCTTCGCTTACACCTCTATTTTGCGCCGTAAAAACACGGCGGTGGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCGACAAAAAc                                                                                     <  2:98027/149‑1 (MQ=18)                                                           cGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAAc                                                                                     >  1:154341/1‑149 (MQ=255)                                                              cTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGTCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTa                                                                                  >  2:287258/1‑149 (MQ=255)                                                                          cTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGaa                                                                          >  5:391399/1‑145 (MQ=255)                                                                          cTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGa                                                                      <  1:287258/149‑1 (MQ=255)                                                                                atTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTca                                                                                                   <  2:290864/114‑1 (MQ=255)                                                                                atTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTca                                                                                                   >  1:290864/1‑114 (MQ=255)                                                                                 ttGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTg                                                               >  6:7802/1‑149 (MQ=255)                                                                                  tGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGt                                                              >  3:68911/1‑149 (MQ=255)                                                                                          acaaacaaGGCGGTCGCGCGCGACTGGTGCAGGAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTacccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaaacctccggcaaacacctcaaaattccaacgccg                                                      <  5:215920‑M2/149‑83 (MQ=255)                                                                                           caaacaaGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCgcggcg                                                       >  4:91089/1‑147 (MQ=255)                                                                                            aaacaaGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCa                                                                                        <  5:357056/113‑1 (MQ=255)                                                                                            aaacaaGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCa                                                                                        >  6:357056/1‑113 (MQ=255)                                                                                                    gggggccgcgcgcCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCcggcg                                            <  6:34673/143‑1 (MQ=255)                                                                                                     ggTCGCGCGCGACTGGTGCAGGAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTacccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctcc                                                                                 <  1:262891‑M2/111‑56 (MQ=255)                                                                                                     ggTCGCGCGCGACTGGTGCAGGAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTacccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctcc                                                                                 >  2:262891‑M2/1‑56 (MQ=255)                                                                                                       tCGCGCGCGACTGGTGCAGGAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTacccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaaacctccggcaaacacctcaaaattccaacgccgtccactcaaaatt                                         >  6:215920‑M2/1‑54 (MQ=255)                                                                                                           gcgcgcCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCgg                                     >  5:389233/1‑149 (MQ=255)                                                                                                               gcCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAgg                                 <  8:224779/149‑1 (MQ=255)                                                                                                                  gggCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGgtcg                              <  2:154341/149‑1 (MQ=255)                                                                                                                     tgcaggAGGGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTacccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctccggcaaacacctcaaaattccaacgccgtccactcaaaattccaacgccgccccc                           >  6:323725‑M2/3‑40 (MQ=255)                                                                                                                      acaGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTcg                                                            >  2:58692/1‑115 (MQ=255)                                                                                                                      acaGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTcg                                                            >  2:53221/1‑115 (MQ=255)                                                                                                                      acaGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTcg                                                            <  1:53221/115‑1 (MQ=255)                                                                                                                      acaGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTcg                                                            <  1:58692/115‑1 (MQ=255)                                                                                                                         ggaggGACTGGCC‑GAAACAAACGTAGGAGCGGGTTTacccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctccggcaaacacctcaaaattccaacgccgtccactcaaaattccaacgccgccccctcaa                       >  8:356525‑M2/1‑36 (MQ=255)                                                                                                                          gaggGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAg                      >  3:103776/1‑149 (MQ=255)                                                                                                                                 tGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGctct               >  8:78713/1‑149 (MQ=255)                                                                                                                                   gCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGctct               <  7:78713/147‑1 (MQ=255)                                                                                                                                     ccGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGgc           >  4:245332/1‑149 (MQ=255)                                                                                                                                     ccGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGgc           >  4:217793/1‑149 (MQ=255)                                                                                                                                      cGAAACAAACGTAGGAGCGGGTTTacccgcgaagcgccgcgcgggcggcgctcgatctcacaggcgctgaaaatcctccggcaaacacctcaaaattccaacgccgtccactcaaaattccaacgccgccccctcaaaattccaacgcc           <  5:347529‑M2/149‑126 (MQ=255)                                                                                                                                           cAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGGCGcttg      >  3:36706/1‑148 (MQ=255)                                                                                                                                            aaaTGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGCTGGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGGCGcttgc     >  1:254000/1‑149 (MQ=255)                                                                                                                                            aaaTGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGGCGcttgcc    >  7:145266/1‑149 (MQ=255)                                                                                                                                              aTGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGGCGcttgccct  >  6:307413/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                                     GCAAGCTCGCTCCTACATTTGTTTCGGGCCAGTTATTCCTGCGGGATTTACGCGCGACCGCCTTCGCGTACACCTCGATATTGCGCCGTACAAACAAGGCGGTCGCGCGCGCCGGGCACAGGAGGGACTGGCCCGAAACAAATGTAGGAGCGAGCTTGCTCGCGATGCGCCGCGC‑GGGCGGCGCTCGATCTCACAGGCAACGCAAACCTATCGCCGAACAGATCAACTGTCGCGGCGCAGGTCCGGCGGGATCGGCAGGTCGTCCTTCAGTGGCTCTGGGCGCTTGCCCT  >  NC_002947/4945216‑4945505

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: ‑