Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,950,953	T→G	7.5%	intergenic (‑103/+54)	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	4,950,953	0	T	G	7.5%	142.4 / 2.6	51	intergenic (‑103/+54)	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
Reads supporting (aligned to +/- strand):  ref base T (23/24);  new base G (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTTGCCTTTAGTGGCGGGGTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCC  >  NC_002947/4950805‑4951091                                                                                                                                                      |                                                                                                                                            gTTTGCCTTTAGTGGCGGGGTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGt                                                                                                                                             >  7:31766/1‑149 (MQ=255)          tAGTGGCGGGGTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGCTGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGc                                                                                                                                       <  1:97710/147‑1 (MQ=255)            gTGGCGGGGTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGcttctt                                                                                                                                  <  5:364170/149‑1 (MQ=255)               gCGGGGTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTcgc                                                                                                                               <  4:290252/149‑1 (MQ=255)               gCGGGGTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTcgc                                                                                                                               >  2:108706/1‑149 (MQ=255)                  gggTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGcttct                                                                                                                                   <  2:70371/142‑1 (MQ=255)                  gggTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGcttct                                                                                                                                   >  1:70371/1‑142 (MQ=255)                       tttGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGc                                                                                                                       >  2:341636/1‑149 (MQ=255)                         tGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGGGCTGGCTTCTTCGCGGGCGAGccc                                                                                                                     >  3:138054/1‑149 (MQ=255)                             tGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCcgcg                                                                                                                  >  2:109284/1‑148 (MQ=255)                               cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaa                                                                                                                <  6:110547/148‑1 (MQ=255)                               cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaa                                                                                                                <  8:47919/148‑1 (MQ=255)                               cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaa                                                                                                                <  3:295745/148‑1 (MQ=255)                               cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaa                                                                                                                <  8:31766/148‑1 (MQ=255)                                ttCGCTCATCGCCATGCCAATAATCCGTCGACCATCGGGGGTTCAAAGGAGAATGGCATGGCTAGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTCCTGGCTTCTTCGCGGGCTCGCCCGTgaag                                                                                                               >  2:114387/1‑148 (MQ=255)                                 tCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                             >  6:23108/1‑149 (MQ=255)                                  cGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaaga                                                                                                              <  1:108706/147‑1 (MQ=255)                                    ctctTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGGGCTGGCTTCTTCGCGGGCGAGCCCGCga                                                                                                                 >  4:55102/1‑142 (MQ=255)                                    ctctTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGGGCTGGCTTCTTCGCGGGCGAGCCCGCga                                                                                                                 <  3:55102/142‑1 (MQ=255)                                       ttCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAagccagc                                                                                                       >  7:32630/1‑149 (MQ=255)                                          gCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                             <  2:270384/140‑1 (MQ=255)                                          gCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaagaa                                                                                                             >  1:270384/1‑140 (MQ=255)                                                  aataatCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGAAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACa                                                                                           >  3:253209/1‑149 (MQ=255)                                                     aatCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGATGAAGCCAGCCC‑AGGCCAACAGtt                                                                                        <  1:341636/149‑1 (MQ=255)                                                       tCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTa                                                                                       >  3:215376/1‑148 (MQ=255)                                                       tCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTAt                                                                                      <  1:109284/149‑1 (MQ=255)                                                        ccGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTAt                                                                                      >  6:214086/1‑148 (MQ=255)                                                             gtcCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCg                                                                                <  7:79382/149‑1 (MQ=255)                                                                 aTCGGGGGTTAAAAGGAGAATGGCTTGGCTTGAGCAAG‑TCTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCACGCGAAGAATCCAGCCC‑ACGACAAAAGTTTTCacgactag                                                                             >  7:129451/1‑141 (MQ=255)                                                                         ttCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGAcc                                                                    >  8:98133/1‑149 (MQ=255)                                                                            aaaGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑a                                                                                                   >  8:185071/1‑115 (MQ=255)                                                                            aaaGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑a                                                                                                   <  7:185071/115‑1 (MQ=255)                                                                            aaaGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGc                                                                  >  5:384246/1‑148 (MQ=255)                                                                              aGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACt                                                               >  2:1776/1‑149 (MQ=255)                                                                              aGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACt                                                               <  1:1776/149‑1 (MQ=255)                                                                                   attgctttggcttcACCATG‑TGTTATCCCAGATTTGGCTGGGGATGCATTCCCGCCGGTTTGGCGGGGCGGGCTTCTTCGCGGGCGCCCCCGCTAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCg                                                           <  2:132943/142‑1 (MQ=255)                                                                                   aaTGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCg                                                           >  1:132943/1‑148 (MQ=255)                                                                                       gcttggcttgAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGa                                                       <  4:215376/148‑1 (MQ=255)                                                                                               gtaGCATG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAaccacc                                               <  2:333018/146‑1 (MQ=255)                                                                                                  gCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGCCCGCACTGTCGCCGACAACCACctgct                                           >  4:36739/1‑149 (MQ=255)                                                                                                      g‑tgtTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑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)                                                                                                                                                      |                                                                                                                                            GTTTGCCTTTAGTGGCGGGGTCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAG‑TGTTATGCCAGATTTTGCAGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCC‑AGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCC  >  NC_002947/4950805‑4951091

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: ‑