Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,950,972	T→G	11.1%	intergenic (‑122/+35)	fliL ← / ← fliK	flagellar protein FliL/flagellar hook‑length control protein FliK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,950,972	0	T	G	11.1%	129.5 / 7.8	53	intergenic (‑122/+35)	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
Reads supporting (aligned to +/- strand):  ref base T (27/20);  new base G (2/4);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 3.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01

TTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCGG  >  NC_002947/4950827‑4951119                                                                                                                                                  |                                                                                                                                                     tttGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGc                                                                                                                                                   >  2:341636/1‑149 (MQ=255)   tGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGGGCTGGCTTCTTCGCGGGCGAGccc                                                                                                                                                 >  3:138054/1‑149 (MQ=255)       tGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCcgcg                                                                                                                                              >  2:109284/1‑148 (MQ=255)         cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaa                                                                                                                                            <  3:295745/148‑1 (MQ=255)         cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaa                                                                                                                                            <  8:47919/148‑1 (MQ=255)         cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaa                                                                                                                                            <  6:110547/148‑1 (MQ=255)         cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaa                                                                                                                                            <  8:31766/148‑1 (MQ=255)          ttCGCTCATCGCCATGCCAATAATCCGTCGACCATCGGGGGTTCAAAGGAGAATGGCATGGCTAGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTCCTGGCTTCTTCGCGGGCTCGCCCGTgaag                                                                                                                                           >  2:114387/1‑148 (MQ=255)           tCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                                                         >  6:23108/1‑149 (MQ=255)            cGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaaga                                                                                                                                          <  1:108706/147‑1 (MQ=255)              ctctTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGGGCTGGCTTCTTCGCGGGCGAGCCCGCga                                                                                                                                             >  4:55102/1‑142 (MQ=255)              ctctTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGGGCTGGCTTCTTCGCGGGCGAGCCCGCga                                                                                                                                             <  3:55102/142‑1 (MQ=255)                 ttCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAagccagc                                                                                                                                   >  7:32630/1‑149 (MQ=255)                    gCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                                                         <  2:270384/140‑1 (MQ=255)                    gCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                                                         >  1:270384/1‑140 (MQ=255)                            aataatCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGAAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACa                                                                                                                       >  3:253209/1‑149 (MQ=255)                               aatCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGATGAAGCCAGCCC‑AGGCCAACAGtt                                                                                                                    <  1:341636/149‑1 (MQ=255)                                 tCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTa                                                                                                                   >  3:215376/1‑148 (MQ=255)                                 tCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTAt                                                                                                                  <  1:109284/149‑1 (MQ=255)                                  ccGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTAt                                                                                                                  >  6:214086/1‑148 (MQ=255)                                       gtcCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCg                                                                                                            <  7:79382/149‑1 (MQ=255)                                           aTCGGGGGTTAAAAGGAGAATGGCTTGGCTTGAGCAAGTCTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCACGCGAAGAATCCAGCCC‑ACGACAAAAGTTTTCacgactag                                                                                                         >  7:129451/1‑141 (MQ=255)                                                   ttCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGAcc                                                                                                >  8:98133/1‑149 (MQ=255)                                                      aaaGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑a                                                                                                                               <  7:185071/115‑1 (MQ=255)                                                      aaaGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑a                                                                                                                               >  8:185071/1‑115 (MQ=255)                                                      aaaGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGc                                                                                              >  5:384246/1‑148 (MQ=255)                                                        aGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACt                                                                                           >  2:1776/1‑149 (MQ=255)                                                        aGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACt                                                                                           <  1:1776/149‑1 (MQ=255)                                                             attgctttggcttcACCATGTGTTATCCCAGATTTGGCTGGGGATGCATTCCCGCCGGTTTGGCGGGGCGGGCTTCTTCGCGGGCGCCCCCGCTAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCg                                                                                       <  2:132943/142‑1 (MQ=255)                                                             aaTGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCg                                                                                       >  1:132943/1‑148 (MQ=255)                                                                 gcttggcttgAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGa                                                                                   <  4:215376/148‑1 (MQ=255)                                                                         gtaGCATGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAaccacc                                                                           <  2:333018/146‑1 (MQ=255)                                                                            gCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGCCCGCACTGTCGCCGACAACCACctgct                                                                       >  4:36739/1‑149 (MQ=255)                                                                                gtgtTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTc                                                                   <  1:63012/149‑1 (MQ=255)                                                                                      tGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAgg                                                             >  7:184969/1‑149 (MQ=255)                                                                                           gATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGAGCGCGAAGAAGCCAGCCG‑AGGCGATAAGTTATCAGGCGGAGTAATCGACCGCCCTGTCGCCGACCACCACCGGCGGCTCCAACGGCCggg                                                        >  2:96589/1‑149 (MQ=255)                                                                                                  cAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATc                                                 <  2:66664/149‑1 (MQ=255)                                                                                                   aGGGGATGGATTCCAGCAGGTTTTCCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCg                                                <  5:77636/149‑1 (MQ=255)                                                                                                    ggggATGGATTGCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGa                                               <  4:253209/149‑1 (MQ=255)                                                                                                     gggATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCGACAGTTATCAGGCGGAGTAATCGCCCGCACTGTCGCCGACACCCCCCTGCGGCTCCCCAGGCCGGGCGCTATCGAc                                              >  4:272297/1‑149 (MQ=255)                                                                                                         tggatTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCt                                          >  2:284694/1‑149 (MQ=255)                                                                                                           gatTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCtt                                         <  5:23108/148‑1 (MQ=255)                                                                                                           gatTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTc                                        <  6:384246/149‑1 (MQ=255)                                                                                                                 agcagGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCTCGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGccc                                   >  1:102554/1‑149 (MQ=255)                                                                                                                     ggTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCAccc                              <  7:98133/149‑1 (MQ=255)                                                                                                                                 cTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGGCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCgg                  >  5:179996/1‑149 (MQ=255)                                                                                                                                      ttcttcGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGgcgcgc             >  3:234661/1‑149 (MQ=255)                                                                                                                                        cttcGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgccg           >  6:212181/1‑149 (MQ=255)                                                                                                                                        cttcGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgcc            <  5:214086/148‑1 (MQ=255)                                                                                                                                         ttcGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCCCCTGCTGCTCCAAAGGCCGGGCGCTATCGACGGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgccgc          >  4:205581/1‑149 (MQ=255)                                                                                                                                          tcGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgccgc          >  6:33176/1‑148 (MQ=255)                                                                                                                                           cgcgGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCa        >  4:35441/1‑149 (MQ=255)                                                                                                                                                 cTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCgg  <  5:33176/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                     TTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCGG  >  NC_002947/4950827‑4951119

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: ‑