Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,016,095	G→A	L76L (CTG→CTA)	fliH →	negative regulator of FliI ATPase activity

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,016,095	0	G	A	100.0%	144.0 / NA	45	L76L (CTG→CTA)	fliH	negative regulator of FliI ATPase activity
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (24/21);  total (24/21)

TGAAGAGGCTGAACCCAGCCTTGAGCAGCAACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTGGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATAGCGTCGCGCCTG  >  NC_000913/2015966‑2016227                                                                                                                                   |                                                                                                                                     tGAAGAGGCTGAACCCAGCCTTGAGCAGCAACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAgggg                                                                                                                             >  2:789546/1‑139 (MQ=255)   aaGAGGCTGAACCCAGCCTTGAGCAGCAACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCt                                                                                                                           >  1:547207/1‑139 (MQ=255)       ggCTGAACCCAGCCTTGAGCAGCAACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAg                                                                                                                       <  1:116939/139‑1 (MQ=255)                 aGCCTTGAGCAGCAACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTgg                                                                                                             >  2:512178/1‑139 (MQ=255)                  gCCTTGAGCAGCAACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGc                                                                                                            >  2:360475/1‑139 (MQ=255)                          cagcaACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGa                                                                                                    <  1:339939/139‑1 (MQ=255)                             caACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGt                                                                                                 >  2:243165/1‑139 (MQ=255)                             caACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAACCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGt                                                                                                 >  2:504622/1‑139 (MQ=255)                                  ggCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTcaa                                                                                            >  1:172234/1‑139 (MQ=255)                                    cgcAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTcaaca                                                                                          <  1:613785/139‑1 (MQ=255)                                                  cAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATg                                                                            <  1:798064/139‑1 (MQ=255)                                                    ggCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGcc                                                                          >  1:668197/1‑139 (MQ=255)                                                      cccATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCg                                                                        >  1:131119/1‑139 (MQ=255)                                                      cccATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCg                                                                        <  1:504622/139‑1 (MQ=255)                                                         aTGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGAt                                                                     <  2:405494/139‑1 (MQ=255)                                                          tGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCg                                                                                                     >  1:201439/1‑106 (MQ=255)                                                          tGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCg                                                                                                     <  2:201439/106‑1 (MQ=255)                                                          tGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATg                                                                    >  1:678550/1‑139 (MQ=255)                                                           gAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAAGGGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATg                                                                    >  2:173118/1‑139 (MQ=255)                                                                aGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCaa                                                              >  2:722364/1‑139 (MQ=255)                                                                aGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCaa                                                              <  1:722364/139‑1 (MQ=255)                                                                           cGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGa                                                   >  1:425622/1‑139 (MQ=255)                                                                           cGGGTATGGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGa                                                   >  1:526908/1‑139 (MQ=255)                                                                            gggTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGaa                                                  >  2:586294/1‑139 (MQ=255)                                                                                    ccGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAAc                                          <  1:789546/139‑1 (MQ=255)                                                                                            cGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTg                                  <  2:87431/139‑1 (MQ=255)                                                                                            cGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTg                                  <  2:131119/139‑1 (MQ=255)                                                                                             gCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGa                                 <  1:586294/139‑1 (MQ=255)                                                                                              ccAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGAt                                <  2:444605/139‑1 (MQ=255)                                                                                              ccAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGAt                                <  2:678550/139‑1 (MQ=255)                                                                                              ccAGCAA‑GGTCATAAGCAGGGCTATCAGCAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGAt                                <  2:481905/139‑1 (MQ=255)                                                                                               cAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATg                               <  1:243165/139‑1 (MQ=255)                                                                                                       gTCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGa                        <  2:547207/139‑1 (MQ=255)                                                                                                        tCATAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGAt                       <  1:360475/139‑1 (MQ=255)                                                                                                          aTAAGCAGGGCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAg                     >  1:452147/1‑139 (MQ=255)                                                                                                                 gggCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATa              >  1:363131/1‑139 (MQ=255)                                                                                                                  ggCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAAtt                                                                                <  1:360977/72‑1 (MQ=255)                                                                                                                  ggCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAAtt                                                                                >  2:360977/1‑72 (MQ=255)                                                                                                                  ggCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATAg             >  2:293853/1‑139 (MQ=255)                                                                                                                  ggCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATAg             >  2:123367/1‑139 (MQ=255)                                                                                                                  ggCTATCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATAg             >  1:475087/1‑139 (MQ=255)                                                                                                                  ggCTAGCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCt                                    >  1:487163/1‑116 (MQ=255)                                                                                                                  ggCTAGCAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCt                                    <  2:487163/116‑1 (MQ=255)                                                                                                                        cAGGAAGGACTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATAGCGTcgc       <  2:172234/139‑1 (MQ=255)                                                                                                                             aggaCTAGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATAGCGTCGCGCCTg  >  2:670120/1‑139 (MQ=255)                                                                                                                                   |                                                                                                                                     TGAAGAGGCTGAACCCAGCCTTGAGCAGCAACTGGCGCAACTGCAAATGCAGGCCCATGAGCAAGGTTATCAGGCGGGTATTGCCGAAGGTCGCCAGCAA‑GGTCATAAGCAGGGCTATCAGGAAGGACTGGCCCAGGGGCTGGAGCAAGGTCTGGCAGAGGCGAAGTCTCAACAAGCGCCAATTCATGCCCGGATGCAGCAACTGGTCAGCGAATTTCAAACTACCCTTGATGCACTTGATAGTGTGATAGCGTCGCGCCTG  >  NC_000913/2015966‑2016227

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑